Kids from all over town converge to play Vanguard, a card game that seems to be the biggest thing going around. A timid boy, Aichi Sendō, has a rare card, the Blaster Blade, which makes him a target for Katsumi Morikawa, a player who wants to use Aichi's card to get revenge on another player, Toshiki Kai. After school, Morikawa and his buddy Yūta Izaki steal Aichi's Blaster Blade from him. Aichi runs to a card shop called Card Capital to find that Morikawa lost it in a bet against Kai. It is then that Aichi and Kai meet and play a round of Vanguard with Blaster Blade as the prize. Before the match, Kai gives Aichi Blaster Blade in the hopes of him using it effectively against him. During the course of the match, Kai teaches Aichi the rules of playing Vanguard. As the fight goes on, Aichi reveals that he has met Kai before when summoning his ace, Blaster Blade, which Kai gave to him long ago, stating that it was because of him that he wants to learn more about Vanguard.

After Aichi plays Blaster Blade, he and Kai recall their first meeting. Back then, after seeing a young Aichi beaten up, the young Kai cheered him up by giving him Blaster Blade, and he told Aichi to imagine himself as a strong warrior like the card. With that in mind, Aichi got absorbed into Vanguard, creating his own deck in the hopes of playing against Kai, who had already moved away by then. Back to the game, Aichi deals a bit of damage to Kai, who retaliates with his ace card, Dragonic Overlord. It wipes out Aichi's units and greatly damages him. All seems lost until Aichi draws a "Heal Trigger", which allows Aichi to stay in the game for one last turn. Aichi launches a final attack with Blaster Blade, which breaks through Kai's defenses and deals one more point of damage to Kai, thus giving Aichi the win. A day later, Aichi revisits the card shop. Despite thinking that Kai would not show up after being defeated, Aichi is glad to see that Kai returns.

Aichi's little sister, Emi, is worried by Aichi's different behavior as of late. After school, Emi sees Aichi with Morikawa and Izaki, who want him to go with them to the Card Capital. However, Emi misinterprets the situation as Aichi hanging with the wrong crowd. Concerned for her brother, she secretly follows the trio to the Card Capital. There, Emi is astounded by all the people in the shop, icluding Aichi, Morikawa, and Izaki, playing Vanguard. It is then that the card shop's manager, Shin Nitta, appears and introduces Emi to the world of trading card games. Emi and Shin then observe a cardfight between Aichi and Morikawa. The battle ends with Aichi winning without taking any damage. Watching Aichi play, Emi sees how much her big brother has changed because of Vanguard. And so, she has become supportive of Aichi playing the game.

After taking a look at Aichi's deck, Shin decides to show him "something nice". So, Shin has Aichi battle Misaki, who, despite working at the card shop, has never actually participated in a Vanguard fight before. Nonetheless, after Shin gives Misaki a special deck, she and Aichi begin their cardfight. In the midst of the battle, Misaki shows that she knows more about the game than she lets on as she draws multiple cards and calls her ace card, the Grade 3 CEO Amaterasu. Using the "Twin Drive" ability that Grade 3 cards have, Misaki defeats Aichi. Through this loss, Aichi learns that he has much more to know about Vanguard if he ever wants to play against Kai again.

Aichi goes to the card shop to buy a booster pack in the hopes of getting a Grade 3 card. When he arrives, he sees a grade-school kid, Kamui Katsuragi, convincingly defeating Izaki in a cardfight. Aichi challenges Kamui, but he refuses, noticing that Aichi is not a strong player. Then, after Kamui beats Morikawa in a cardfight, Aichi tries to buy a booster pack. Suddenly, Emi appears, and Kamui immediately falls in love with her. Before Aichi could buy a pack, Emi drags him back home while Kamui looks on, thinking that the two are boyfriend and girlfriend. Later, Aichi buys a booster pack and is pleased to find that the pack contained a Grade 3 card, Solitary Knight, Gancelot. Just then, Kamui shows up and challenges Aichi, demanding to get Emi if he beats him. Although Aichi misunderstands Kamui's intentions, he and Kamui begin their Vanguard fight. Kamui uses powerful cards like Genocide Jack and King of Swords to quickly deal a ton of damage to Aichi, who strikes back by using his newly-acquired Solitary Knight, Gancelot. But in the end, Aichi loses to Kamui after he calls his ace card Asura Kaiser. Afterwards, Emi arrives and tries to get Aichi home, and it is then that Kamui learns that the two are actually siblings. Now, hoping to get closer to Emi, Kamui starts referring to Aichi as his "big brother", although Aichi is not exactly glad about it.

Aichi and his friends decide to go to a different card shop called PSY. There, they try out the shop's special Vanguard Fight Stage. It oddly reacts to Aichi, which leads to a woman, Kourin, challenging him to a cardfight. When the two begin the battle, Aichi is surprised that the stage brings the cards to life. Aichi and Kourin, who both use a Royal Paladin deck, continue their battle, until Aichi makes a bad decision in not guarding one of her Vanguard's attacks, ultimately leading to his defeat. Afterwards, another woman, Suiko, gives Aichi the card The King of Knights, Alfred as a special memento for visiting the card shop. Later, Aichi learns from Morikawa that the card shop they visited has disappeared.

Shin introduces the "Standing Fight Table (Name Subject To Change)" to enrich the experience of a Vanguard fight, with Morikawa and Kamui being the first to play on it. After Kamui once again beats Morikawa, Aichi and his friends return to their homes but then see Kai walking back to his home. Wanting to learn where Kai lives, Aichi, Kamui, and Miwa try to follow him, but Kai soon notices them tailing him. Aichi apologizes and tries to get Kai to battle him again, but he declines. However, Kamui challenges Kai, and he reluctantly accepts. The next day, the two commence their cardfight. Kai gains the upper hand by getting a Grade 3 card, Embodiment of Victory, Aleph, into play before Kamui, who counterattacks with his own Grade 3 unit Mr. Invincible. But Kai soon summons another Grade 3 unit Vortex Dragon, and he later activates its Soul Blast skill to destroy some of Kamui's units, leaving Kamui unable to defend himself from Kai's final attacks. Kai defeats Kamui and takes his leave, but not before Aichi tells him that he'll become a stronger and more worthy opponent for him.

The Card Capital Shop Tournament begins soon, but Aichi is hesitant to play in it, even after making a new deck. However, when he learns that Kai will be in the tournament, Aichi decides to enter as well. But when he submits his entry application form, another Vanguard player, Osamu Kishida, places his application at nearly the same time as Aichi. Both of them want to enter, but there is only one open spot left in the tournament. To resolve this issue, Shin recommends to have Aichi and Osamu play against each other to see who gets the last entry spot. Using his Megacolony units' effects, Osamu restricts Aichi's units from standing while scoffing at him for calling so many weak units. However, Aichi uses his new card The King of Knights, Alfred, whose power is increased by the number of other Royal Paladins in play. With Alfred, Aichi defeats Osamu and is therefore officially in the tournament.

The Card Capital Shop Tournament finally begins. In the first round, Aichi must play against Izaki while at the same time, Morikawa battles Misaki. Since this is his first time in a tournament, Aichi grows nervous. His tournament jitters get the better of him as he makes many amateur mistakes. But when he sees that Izaki is also just as nervous and makes similar mistakes, Aichi realizes that he's not alone, regains his composure, and remembers that Vanguard fights should be fun. When he tells Izaki that, he too calms down, and the two continue playing the game at their best. In the end, not only does Aichi win, but Misaki also advances to the next round.

Kamui and Kai advance to the second round of the tournament, along with Ninja Master M, an eccentric player who dresses and acts like a ninja. He meets Aichi, who deduces that he is actually his teacher Mark Whiting, but he denies that claim (even though it's true). The tournament progresses to the second round matches with Aichi facing off against Ninja Master M while Kai plays against the previous tournament's champion Kazuki Inaba. Ninja Master M uses his Nubatama ninja units' effects to deplete the cards in Aichi's hands. He drives Aichi to a corner when he rides his ace card Stealth Dragon Voidmaster and leaves only one card in Aichi's hand. While this is going on, Kai defeats Inaba in his match.

Aichi makes a comeback by calling more units from his deck to boost the power of The King of Knights, Alfred, forcing Ninja Master M to use most of his cards to guard against his attacks. As a result, M is left with no cards to defend himself from Aichi's last attack. Aichi wins and therefore advances to the semifinals. Ninja Master M disappears, and Mark soon arrives (with a bag containing his Ninja Master M attire). After Aichi's match, Kamui and Misaki play in their respective cardfights, and they both advance as well. Before the start of the semifinals, the tournament is put on hold for a lunch break. So, Aichi and Emi have lunch outside the card shop where Kamui tries to get Emi to feed him, but no such luck. After everyone returns to the shop, Aichi, Misaki, Kamui, and Kai all draw lots to determine who will be playing against who. Aichi is put up against Kamui while Kai must fight Misaki. With the matchups set, the semifinals begin.

It's the semifinals: Kai plays against Misaki, and Aichi once again battles Kamui. Both Aichi and Kamui want to win for their own reasons; Aichi wants to fight Kai again while Kamui hopes to gain Emi's affection upon winning the entire tournament. Aichi defends himself from Kamui's Genocide Jack's attacks better than he did in their first cardfight. Aichi makes a surprising move by calling Blaster Blade as a rear-guard and using its ability to destroy Genocide Jack. As the battle between Aichi and Kamui rages on, the cardfight between Kai and Misaki comes to a close with Kai as the victor.

Aichi and Kamui's match comes down to the wire, with Kamui slowly building up his Vanguard's Soul. Despite Aichi getting a Heal Trigger to allow him to stay in the game, Kamui then uses his Mr. Invincible's Soulblast, dubbed the "Tornado Stand Galactica", making all of his units stand up and ready to attack again. With this move, Kamui once again defeats Aichi. After he gets over this loss, the final battle between Kai and Kamui ensues. Even though Kamui uses Mr. Invincible and its Soulblast like in the previous match, Kai nonetheless successfully defends and survives the onslaught. In the end, Kai beats Kamui again and is therefore the champion of the entire tournament. After the tournament, Shin then makes a special announcement: the four finalists (Kai, Kamui, Misaki, and Aichi) of this tournament are to represent Card Capital and participate in the regional tournament, shocking Aichi.

Kamui takes Aichi to Card Shop Handsome, a pirate-themed store that Kamui used to visit. They meet the national-tournament-level and previous regional champions Team Handsome, which is led by Gouki Daimonji. Soon after, they also meet Gouki's little sister Nagisa. She has a huge crush on Kamui to the point that she wants to marry him despite their young age, but he does not feel the same way about her. When Kamui tries to explain that he's in love with Aichi's sister Emi, the situation is misinterpreted as Aichi trying to take away Kamui and hurting Nagisa's feelings. Wanting to make her little sister happy, Gouki challenges Aichi to a Cardfight with the winner getting Kamui. As the fight goes on, Aichi learns the horror of Gouki's Granblue deck as he constantly resurrects his undead pirates from the Drop Zone. The level of a Cardfighter who has played in a national tournament proves to be too much for Aichi; Gouki beats Aichi, learning the level of competition that he will face in the future. After the game, the misunderstanding is cleared, and Nagisa goes back to chasing after Kamui, much to his dismay.

As Emi continues coming to the Card Capital Card Shop, Shin convinces her to try the game out for herself. While approaching the game shop, Katsumi has his fortune told and he finds that he will have luck with his juniors today (however, Yuta corrects him and says that he'll have terrible luck today). When they arrive at the card shop, Aichi is surprised when Emi is preparing to play Vanguard. Emi is handed Misaki's deck as Shin wants both Aichi and Emi to battle together. However, Katsumi wishes to take Aichi's place and a battle between the new player Emi and the "Expert Naive Player" Katsumi begins, with Kamui bitter about how Katsumi is playing against her instead of himself. Despite only using "cute" cards, Emi defeats Katsumi with some beginner's luck.

The day for the regional tournament is here. Shin drives the team of Aichi, Kamui, and Kai to the tournament site. on the way there, while Aichi and Kamui make adjustments to Aichi's deck, Shin decides to name the team "Quadrifoglio" (Italian for "four-leaf-clover"; Q4 for short). They arrive and watch a promotional video of the pop idol group Ultra Rare, who are the three girls, Kourin, Rekka, and Suiko, who Aichi met at the card shop PSY. After a run-in with Team Handsome, it is then accounced that Team Q4 will play in the first round against Team Black Magic, three dark-robed men who all have "Kuro" (Japanese for "black") in their names. Because of Misaki's absence, Aichi will have to participate, and in the first match, too! Aichi's fight does not go well. His opponent, Kurosawa, appears to use the same clan as Kai, the Kagero, but with many new units. When he Superior Rides Demonic Dragon Berserker, Yaksha and uses several skills to retire all of Aichi's Rear-Guards, Aichi panics, realizing that even if he rides Alfred, he cannot use fully use its ability. In a desperate move, he uses all the cards in his hand, including the newly-added Knight of Truth, Gordon, to create an almost full field.

Aichi has difficulty pushing for victory, and his opponent gets a Critical Trigger on top, bringing him to five damage. Aichi desperately needs to block the next strike, but is unwilling to leave his hand empty. He guards with Wingal and Intercepts with his new unit Knight of Truth, Gordon. At first, it seems that Aichi has an insufficient amount of Shield, but he reveals that Gordon's skill, the Especial Intercept, allows its shield to rise by 5000 points during an Intercept. Aichi then proceeds to call Gigantech Charger, another new card whose skill is used to completely fill Aichi's side of the field, and finish the match with a Critical Trigger. Team Black Magic's next fighter, Kurosaki, appears, while on Team Q4's side, Kai steps up. They both use Kagero, and the announcer, MC Miya, and spectators seem to think it will be an exciting match. However, they are soon disillusioned - Kai annihilates his opponent without even breaking a sweat. Afterwards, everyone sees that underneath Team Black Magic's dark cloaks are actually three sparkling-bright young men. Kai's victory leads to Team Q4 advancing to the next round and Kamui becoming enraged that he was not given the chance to fight.

The regional tournament continues with Team Q4 easily plowing through their second and third opponents, Team Martial Arts and Team Chemistry Club, by defeating them both 2-0. Kamui's past relation to Gouki and Team Handsome is revealed, and Gouki and Kamui pledge to be the first to take the stage in the final match. During a break, Emi arrives with lunch, making Kamui happy to eat her food. But this moment is ruined when Nagisa charges in with her own prepared lunch and messes things up for Kamui. Incidentally, both lunches end up in Morikawa's stomach, who spews fire like a dragon from the spicyness of Nagisa's food, which Kamui does not appreciate. After a musical performance by Ultra Rare singing their opening hit song "Miracle Trigger", the tournament finals commence. Kamui, expecting to play against Gouki in the first game, is shocked when Nagisa steps up to be his opponent.

Surprisingly enough, Nagisa steps into the fray as the first fighter of Team Handsome, resulting in Kamui being in a desperate situation as she declares that Kamui has to marry her if she wins. Kamui answers back by declaring that if he wins, then Nagisa will leave him alone. Both parties agree to these terms and then start their Cardfight. Using a Nova Grappler deck like Kamui, Nagisa proves herself to be an excellent fighter, fighting toe-to-toe with him. Though it seems that the agonizing Kamui can make a reversal using Lion Heat, Nagisa is able to fully negate his attacks and finish him off using her own Lion Heat and Magician Girl, Kirara with a "Wedding Hold" during the next turn. After the match, as per agreement, Nagisa gets dressed in a wedding gown and is ready to marry Kamui, who tries to run for his life.

In spite of Nagisa winning and her getting to marry Kamui as a result, Kamui weasels out by saying that Team Q4 as a whole hasn't lost yet, so their agreement is still pending. With one loss in their record, Team Q4 has to win both the next matches in order to advance through the regional tournament. Though everyone is certain that Kai will win, Aichi becomes increasingly desperate, as his match will be the one to decide the fate of the team, going as far as to thinking of running away to have Misaki participate instead. As Kai walks up to play, he indirectly tells Aichi that people who run away are not worthy of fighting him. His opponent, Kaoru "Ka-boom!" Komatsubara, seems to be a formidable opponent who gloats how he's a national-tournament-level player, but Kai gains an early lead, pushing his enemy into a bad situation. Throughout the battle, Kai chooses to not defend against all except one of Kaoru's attacks, puzzling everyone about his decisions. Aichi believes that Kai is trying to tell him something through these actions; he deduces that Kai knows that he does not need to defend and will still be able to win. When both players are at five damage, Kaoru confidently declares that he will survive and claim victory, but Kai refutes that claim, loudly announcing Final Turn! He rides a new card, Blazing Flare Dragon, and uses a card skill to retire one opposing unit and increase its attack power. Kai relentlessly adds to the power by drawing two Critical Triggers in a row, thoroughly annihilating Kaoru. Seeing Kai's power, and remembering his own aspirations to reach his level, Aichi becomes motivated to win his fight!

Aichi's match against Gouki begins. Aichi remembers Gouki as a formidable opponent, and realizes that he cannot stay the same as before if he wishes to win. Using a combination of the skills of Barcgal and Knight of the Future Llew, he Rides Blaster Blade from the deck, surprising Gouki. With both sides getting a Heal Trigger and staying at nearly the same amount of damage, it becomes an intense fight. Gouki Superior Rides Spirit Exceed from the Drop Zone and prepares for a full frontal assault.

The fight between Aichi and Gouki continues. Aichi blocks Gouki's attack, and counterattacks with Alfred, bringing Gouki to five damage. However, Gouki replaces his Vanguard with King of the Demonic Seas, Basskirk, who uses eight cards from the Soul and five cards from the Damage Zone, to instantly revive as many Granblue units from the Drop Zone as possible! Though Aichi perfectly defends during that turn, he realizes that he must finish it immediately. A strange blue light emerges from his deck, which Kai notices. Aichi draws into one of the new cards that he had acquired, which he had put in his deck despite Kamui's advice. He rides Soul Saver Dragon, the powerful God of the Royal Paladin knights, and activates its skill to power up his rear-guard units. Though it seems like Gouki will make it past, Aichi Drive Checks a Stand Trigger, and finishes the game with a brutal attack. With Aichi's win over Gouki, Team Q4 wins the regional tournament and is therefore eligible to enter the national tournament. At the awards ceremony, Ultra Rare congratulates Q4 for their victory, and Suiko invites Aichi to visit PSY once more.

Aichi, Kamui and Misaki visit Card Shop PSY after Suiko's invitation. They meet an aloof red-haired stranger with a peculiar attitude. However, once the Ultra Rare group arrives, they learn that he is none other than Ren Suzugamori, the winner of the previous national tournament! Kourin and Ren engage in a Cardfight, both using the exact same deck structure, and Aichi, who had been beaten by Kourin before, watches in amazement as Ren easily controls the match. Strangely using the same speech patterns that Kai does during his matches, Ren uses a seemingly simple Grade 1 card called Blazer Idols to finish the game. However, what are these visions that Aichi has of the planet Cray, when Ren is about to make his move...?

To prepare for the national tournaments, worried about Cardfighters on Ren's level, Aichi and Misaki engage in a fight. However, memories of her tragic past surface in Misaki's mind, causing her to break down. Though she dominates the match by preventing Aichi's strategy from taking effect until it is too late, and finishing him off by means of a Critical Trigger, she abandons the team directly afterwards, claiming to be unable to fight any longer. Stunned, Aichi and Kamui try to discover what they have done wrong...

Emi visits Card Capital, worrying about the depressed Aichi. She encounters Misaki, who claims not to know anything - but the manager pushes the two into a cardfight using the new trial decks that just arrived. Going along for Emi's sake, Misaki uses the new Nova Grappler deck, whereas Emi uses the Oracle Think Tank one. Already having memorized all effects of the cards with her perfect memory, Misaki easily defeats Emi, but in doing so, she remembers the fun that Vanguard used to be for both her and her parents, and realizes that they would not want her to feel sad about the game. Receiving a key from her uncle to unlock the box with the deck her parents made for her, she rejoins Team Q4 to Aichi and Kamui's joy, who feel terrible about what had happened, and easily beats every regular customer of the shop.

Team Q4 arrives at the site of the national tournament grounds and meets Team Caesar, composed of Kenji "Koutei" Matsusada and the siblings Gai and Yuri Usui, who were the last national tournament's finalists and previous winners. Everything seems to be going well, but due to Kai's increasingly arrogant and insulting attitude, Kamui decides he can no longer work with him and abandons the team. Aichi attempts to go after him, but is reminded that if he also leaves, Team Q4 will be unable to participate in the tournament and will therefore be disqualified. With some advice from Kenji, Aichi decides to win the preliminary rounds and earn Q4 a spot in the finals, so Kamui can return.

The national tournament preliminary rounds begin! After an explanation of the tournament rules by Ultra Rare, Team Q4 discovers that they are put in the same block as Team Foo Fighter Apex Limited Four, Ren Suzugamori's team and previous winners. To his great surprise, Aichi discovers that Kai not only personally knows one of AL4's members, but is also acquainted with Ren. They are soon forced to forget about AL4, though, since the first round begins and pits them against Team Jurassic Army, a group of militaristic Cardfighters using the brutal Tachikaze clan. Aichi takes the first match against Gunji, and though he allows himself to take damage and use the skill of Blaster Blade effectively, he is cornered by the Tachikaze ace, Tyrant, Deathrex...

Gunji brutally corners Aichi with the speed and power of his Tachikaze deck, bringing the score to 5-3 in Gunji's favor. To make a reversal, Aichi rides his new ace card, Soul Saver Dragon. Managing to get a Critical trigger, it looks like the match has been decided, but luck favors Gunji, who gets a last-minute Heal Trigger and survives, winning on the next turn. The next match features Misaki who, despite cleverly using the attribute of Silent Tom to cripple her opponent's ability to guard, is also defeated in the exact same manner. With their first match ending in a brutal defeat, Team Q4 cannot afford to lose again.

Team Q4's second match against Team Muscle Brain begins. Team Muscle Brain believes that training the body will result in a better mind, and thus practices brutal fighting prowess. However, when Kai steps up to the first match, he is able to annihilate his opponent easily by Superior Riding Blazing Flare Dragon. Misaki takes the second match, using a new line of cards located in the deck that was given to her by her parents before their death. Though she can't seem to get a Grade 3 in hand, using the effects of her units she Superior Rides Goddess of the Full Moon Tsukuyomi. Using skills that allow her to draw, she increases her hand to the point where she comfortably blocks her opponent's desperate move, and finishes the game. There is no time to celebrate, though, as the next match is versus Team AL4, the strongest team.

Team Q4's final fight in the preliminary rounds, which they cannot afford to lose, begins. Kai takes the stage first, against AL4 member "Crusher" Kyou Yahagi, who potently uses a Spike Brothers deck. Kai rides Dragonic Overlord and activates its skill, but Kyou blocks it, pushing Kai on the defensive. However, Kai recovers his momentum with a Heal Trigger, allowing him to reclaim three unflipped damage. He uses Overlord's effect once more, annihilating Kyou's defense and claiming victory. An observing Ren claims the result was not unexpected and grins madly, while Kyou runs off in panic.

Though Kai won the first match of the team battle, Misaki is challenged by Asaka Narumi, known as the "Assassin". Asaka skillfully uses a Pale Moon deck, and though Misaki tries to fight by reading her opponent's moves, Asaka plans further ahead and cripples Misaki's strategy while preparing her field. Using an unavoidable three-pronged attack pattern coupled with a Draw Trigger, Asaka delivers the final blow to Misaki. This leaves both teams with a single match won, and it is up to Aichi to determine Q4's fate against Tetsu, the General of AL4. Tetsu, using a Dark Irregulars deck, deals 3 damage to Aichi in his very first turn - however, Aichi has a plan.

The match between Aichi and Tetsu continues while an anxious Kamui watches. Confronted by Nagisa, Gouki and Emi, who learned of the situation via Team Caesar, Kamui is motivated to support Aichi. Aichi begins to make a comeback by shutting down his opponent's offense and evening out the damage with a heal trigger, but Tetsu rides Demon World Marquis Amon, and with a Critical Trigger, pushes Aichi down to five damage. Aichi gains a vision of the Royal Paladin knights joined together, and draws and rides Soul Saver Dragon, whose effect is used to power up all his units. Regardless, Tetsu manages to block, and during his next turn rides Still Vampyr. That card has a deadly effect that replaces the opponent's Vanguard with another Rear-Guard, thus Aichi is forced to ride the Grade 0 Future Knight, Llew. In this weakened form, he is unable to withstand Tetsu's attack and suffers a terrible defeat. It seems as if all hope is not lost, as Jurassic Army loses to Muscle Brain and a 3-way tie is formed. Through a final judges' call based on overall performance, Ultra Rare announces that Jurassic Army is the team that progress. Ren meets up with Q4 and tries to get Kai to rejoin his team, but Kai refuses him, and Ren blames Aichi for Q4's failure.

Team Q4 gathers at Card Capital to watch the national tournament finals. Due to various delays, they only manage to catch the very last match, where Ren, leader of Foo Fighter AL4, faces of against Kenji, leader of Team Caesar. Even though Kenji appears to put up a good fight, Aichi sees right through Ren's power. Ren quickly decides to take the battle a little more seriously, and rides Blaster Dark, a black version of Blaster Blade. In a couple of turns, he completely annihilates Kenji, and AL4 are crowned the national champions. In an attempt to cheer Q4 up, Shin arranges for a beach trip, but Aichi is too demotivated for it. Miwa manages to convince Kai to speak to Aichi. Kai's words give Aichi the motivation to continue playing. Fired up, Q4 requests a special training session from Shin.

Q4 has gone to the beach in order to train at Vanguard - though a lot of its supporters, such as Katsumi, seem to have other priorities. The team meets up with Team Caesar, who set up the training camp, and they quickly engage in cardfights. Surprising everyone, Kai actually defeats Kenji, and the two engage in an elaborate discussion about strategies and tactics. In the meantime, Aichi loses to Yuri five times in a row. Yuri requests to see Aichi's deck, and once she does acknowledges that it's a good deck, but with a weak unifying victory strategy. Aichi thinks about her words as everyone prepares curry for dinner, and while everyone else sleeps, he begins working on his deck.

Aichi sleeps late and is thus the last to get up. Kai and Kenji have woken up before everyone else and are already engaged in Cardfighting. They have leftover curry for breakfast, while Aichi reports the unfortunate results of his deck editing session. They go to the beach, where Aichi, Katsumi and Yūta are put under a special training regimine by Kamui, which culminates in them imagining themselves as valiant Vanguards on Cray. Shin presents Q4 with a briefcase full of rare cards, which they used to build up their decks. Aichi's Royal Paladins speak to him in his mind, and he reconstructs his deck without realizing it. Yuri challenges Aichi to a rematch, and Aichi skillfully uses the effects of Hi-Dog Breeder Akane and Pongal to get Soul Saver Dragon in his hand, before Katsumi interrupts the match. The team finally leaves the training camp, satisfied with the experience they have gathered.

Miwa spys on Kai who has begun fighting in underground fights in order to find stronger opponents. Underground Cardfights usually result in the loss of cards, and players do not abide by the rules that ensure fair play in a Cardfight. When Miwa discovers that Kai is searching for Jun, the King of Underground Fights, he goes looking for him. He confronts Jun, and is captured. Jun and Kai then have a Cardfight with Miwa and Kai's freedom at stake. Jun uses a Dark Irregulars deck against Kai, and puts up a fierce fight by making use of his cards' abilities. At the end, he attempts to use his ace, Edel Rose, and her critical strike ability to finish off Kai, but is prevented by the complete defense of Kai's Wyvern Guard, Barri. Kai and Miwa leave, with Miwa figuring out that he had been used by Kai to draw Jun out.

A tournament is being held again at Card Capital, but it is now a team fight due to the large number of participants. Team Q4 fights and moves all the way up to the final round, with Kai not participating in the team fight. Q4 discovers their opponent to be Team Overthrow which consists of Miwa, Yūta, and Katsumi, who is dressed up as Ninja Master M, since the costume was donated to him by M, since he decided to not participate in tournaments anymore. In the first round, Katsumi faces Misaki and completely loses due to his deck being full of grade 3s. The second round features Kamui and Degozaru's secret weapon, Princess Maiden, who is actually Emi, who wanted to participate in the tournament. Because of Kamui being unwilling to give his all against Emi, she defeats him using her Bermuda Triangle/Oracle Think Tank deck. Now it is Aichi's turn, and his opponent is none other than Miwa!

The fight between Miwa and Aichi begins. Miwa, who surprisingly uses a Kagero deck like Kai, forces Aichi into a corner by using powerful retiring strategies, and even though Aichi manages a powerful attack using two Pongal and Young Pegasus Knight, and then Solitary Knight, Gancelot as well as Soul Saver Dragon, Miwa blocks his efforts, and calls Dragonic Overlord, activating its Eternal Flame. Though Miwa gloats with 'Final Turn', Aichi blocks his attack, and then places down Flash Shield, Iseult to neutralize Overlord's hit. He proceeds to win the game using Soul Saver Dragon - however, Kai is informed by Miwa that Aichi hears the call of card spirits, which greatly worries him.

The regionals commence once again, with Team Q4 and Team Handsome competing. Battles rage as Team Handsome advances to the next round. Team Q4's first opponent, though, is Team Fragrance, a dangerous group whose members claim to be able to sense their opponent's feelings by their scent. Aichi displays extraordinary positiveness by claiming the first spot for Q4, and proceeds to the fighting arena.

Aichi trusts the voice of his cards, riding Solitary Knight, Gancelot and calling King of Knights, Alfred to the Rear-Guard circle. His opponent uses an Oracle Think Tank deck. Though his first Counter Blast with Gancelot is thwarted by Chocolat, he tries again during the next turn, and scores an unexpected Critical trigger, winning the match. Misaki proceeds to win the second fight with a clever combination of Oracle Guardian Red-Eye and Goddess of the Full Moon Tsukuyomi. Team Q4 also advances, but Aichi seems exhausted from his previous fight and collapses, unable to continue. The next fights are conducted without his presence, and Kamui and Kai easily dominate their opponents, allowing Q4 to move once more to the very last round, where they hope to face Team Handsome. However, Gouki and the others are defeated by a mysterious team called Avengers, whose leader is revealed to be none other than "Crusher" Kyou Yahagi, seeking revenge against Kai...

Kyou is back for revenge against Team Q4 - specifically Kai. Kyou then proceeds to explain how things came to be this way - since he lost his match to Kai during the Nationals, he got banished from AL4. As a former member of AL4, Kyou had trouble finding a new team to join because no one wants to recruit a discarded AL4 member to prevent any conflicts. After multiple rejections, Kyou goes insane and swears vengeance against Team Q4. For the first match, Aichi decides to take the lead instead of letting Kai face Kyou again in hopes of earning more of Kai's acknowledgement. Under the influence of his new powers, Aichi becomes a completely different Cardfighter. Before the match, Aichi declares his victory and the card Young Pegasus Knight as the key card to win the match - something that Ren would do. During the match, Kyou slowly becomes intimidated by Aichi's resemblance to Ren. Kyou believed Aichi was simply bluffing after retiring his Young Pegasus Knight during his second turn. But at the end, Aichi reveals the second Young Pegasus Knight he had and declared his victory with the same attitude and aura as Ren.

After easily blocking Kyou's quadruple attack, Aichi declares 'Final Turn'. Though it seems his plan is going to be defeated, thanks to a Stand trigger, Aichi manages to deliver the finishing blow using Young Pegasus Knight. It is determined by Suiko that Aichi possesses the ability PSY Qualia, which they seek. Kyou has a vision of planet Cray, where he is slashed down by Pegasus Knight, and collapses, obliterated. Similarly, an exhausted Aichi falls in Kai's arms, and he is brought to the infirmary. The second match between Misaki and Team Avenger's second member begins. Aichi is visited by Emi, who claims Aichi looked scary during his fight, though Aichi doesn't notice anything different. Misaki wins her fight, though Suiko and the others decide she doesn't possess the ability PSY Qualia. Aichi is visited by Kai, and although he seeks his approval for becoming stronger, Kai calls him weak, and abandons him and Team Q4 after Aichi challenges him to a fight in order to prove his strength. Kyou continues seeking his revenge, until Team Brilliant Stars appears, ordering Kyou and the others to be arrested.

Kamui is concerned when Aichi stops coming to Card Capital after the tournament. Aichi continues to be haunted by Kai's words and finds himself unexpectedly at the door to the PSY Card Shop. Aichi enters the shop and is greeted by the members of Ultra Rare where he asks them if he was strong in the last tournament. Everyone is then surprised when Ren enters the shop. Confronting Aichi, Ren explains what has been happening to him lately and the nature of the power, PSY Qualia. Ren tells Aichi that Kai will only acknowledge strong fighters and that he must get stronger. Ren then gives Aichi a Shadow Paladin Deck, the dark opposite of his Royal Paladin Deck. Seeing through PSY Qualia, Aichi is nearly overwhelmed by the deck's power and believes this new deck makes him invincible. Kourin believes he's being arrogant and challenges him to a duel with her Royal Paladin Deck. In the match, Kourin is easily and soundly defeated by Aichi using Blaster Dark and his new Shadow Paladins, demonstrating the fearsome power of PSY Qualia. All the while, Ren watches from the shadows, smiling and encouraging Aichi to embrace his new dark power.

After losing to Aichi, Kourin goes to Card Capital, asking for Kai. Since Miwa is the only person who knows where Kai is, he rides with Kourin to the Underground cardfight area. They find Kai, who is beating all the underground fighters to relieve his frustrations. Kourin soon challenges him to a fight, where Miwa and Jun get to sit in the middle of the action. While Kourin uses her Royal Paladin deck, Kai reveals his newly modified Kagero deck, which focuses on Amber Dragons. As each of them are dealing damage to each other, Kourin confronts Kai about how it's his fault that Aichi has fallen into the power of Psy Qualia, saying that Aichi only sought the power because he wanted to become stronger for Kai's approval. Kai agrees, and also claims that he had seen the corrupted effects of Psy Qualia before, not knowing how to prevent it from happening. He then tells Kourin that it may have been one simple thing: to exceed that power. Kourin then asks Kai if he can stop Aichi before he falls completely under the influence of Psy Qualia, to which Kai says that he can. After losing to Kai, Kourin gives him Aichi's Royal Paladin deck, and hopes that he can succeed where she had failed. Meanwhile, Aichi spends the entire night in his room, mentally preparing himself for the National Tournament. When arriving at the tournament, Aichi tells Kamui to relax as he is sure that they will win, revealing his newly acquired Shadow Paladin deck, much to the shock of his teammates.

At the start of the tournament, Team Q4 is placed in the same block as Team Jurassic Army and Team Brilliant Stars, another faction of Foo Fighters. After having a brief conversation with Team Q4, Kiriya Bidou, leader of Brilliant Stars, is summoned by Ren, who tells him that if he can take care of Aichi, then he will be allowed into AL4. When Team Q4 is getting ready to face Jurassic Army, they are greeted by the members of Team Caesar, who wish them luck to meet in the finals. Aichi then claims that even without luck, they will be at the finals, since their victory is guaranteed, puzzling Team Caesar. As he steps onto the field, Aichi is once again faced off against Gunji, who asks if he has gotten stronger since their last match. Fed up with people asking how much stronger he has gotten, Aichi tells Gunji that it is best to just show much power he has, and warns him that he will soundly defeat him. Using his new Shadow Paladin deck, Aichi beats Gunji, despite drawing a heal trigger like last time. Although Gunji claims that Aichi has gotten stronger, it is not something that should be praised for. Soonafter, Ren claims that Aichi still has not released his true powers, as Aichi once again collapses from using Psy Qualia. As Aichi is resting in the infirmary, both Kamui and Misaki agree that till the finals, they would not let Aichi fight again, while Kourin returns, hoping that Kai will make it in time to help Aichi.

After defeating Jurassic Army, Team Q4 are now up against Team Spyder, and Kamui easily defeats his opponent using Stern Blaukruger, despite being tricked throughout his match. Misaki is up next, but her opponent uses data to attack and uses the skills of deadly cards like Elite Mutant, Giraffa and Ant Lion to choose units from Misaki's field to not stand next turn. Even with that, she drew Goddess of the Full Moon, Tsukuyomi and uses counterblast to replace all her rear-guard units. With that, they move on to face their last opponents in the C Block, FFBS (Foo Fighter Brilliant Stars).

Team Q4 proceed to fight Team FFBS and Kamui is up first, facing Hiromi from FFBS. Hiromi then used the skills of Young Pegasus Knight, Hi-Dog Breeder Akane, Great Sage Barron, Knight of God-speed Galahad and Margal to power up her units. Kamui skillfully defends and used the skill of Stern Blaukruger to stand Stern and the unit behind him to finish the fight. Hiromi congratulates Kamui about winning the first fight, but tells him that their victory as a team had vanished. Aichi then wakes up and manages to watch Misaki's fight, and found out that Misaki had lost the match due to Sealed Dragon Blockade, a vicious card that disables Misaki's rear-guards to intercept. After watching the fight, Aichi slowly makes his way to the fighting area to start the third fight. As he walks towards the Motion Figure System, Shin, Misaki and Kamui were shocked. Aichi tells Misaki and Kamui that he was disappointed in the two and gave them and confident, evil smile. His opponent, Kiriya Bidou told Aichi he was convinced that Aichi would run away and Aichi replied, saying that there was no need to be afraid of him. The fight begins!!

As the fight between Kiriya and Aichi begins, Kai is seen watching the match in another area. Emi runs to Team Q4, worried about Aichi playing in another fight, but finds both Misaki and Kamui visibly shaken from Aichi's words. While the fan girls for Brilliant Stars are cheering, Kiriya is still wondering if Aichi has really mastered the Shadow Paladin Deck, while deciding to prove his worth by beating him in front of Ren. With his Pale Moon Deck, Kiriya successfully deals damage to Aichi with his Juggler cards and calling cards from the Soul. Aichi simply takes a few damage and defends himself with a couple of cards, all while taunting Kiriya about Ren giving him the Shadow Paladin Deck because he is strong. After riding Dark Illusionist, Robert, Kiriya is able to deal three damage to Aichi, giving him almost complete control of the match. However, as Miwa states, Aichi is just playing around with Kiriya, as he rides Phantom Blaster Dragon, and calls Blaster Dark to the rear guard to help deal damage. Kiriya is able to defend himself, allowing only one damage as he eagerly calls "Final Turn" on Aichi. With Ren watching, Kiriya stands in shock as Aichi completely defends himself and takes no damage. Wondering if Kai is watching his fight, Aichi claims he will show how strong he is, calling his "Final Turn" on Kiriya. Calling two more Grade 3 units, Aichi soundly defeats Kiriya, while still muttering that he needs to be even stronger for Kai's recognition. As everyone in the stadium cheers Team Q4 for winning the elimination rounds, Ren congratulates Aichi for winning, while forgetting who Kiriya is. Meanwhile, Kai is seen walking away from watching the match, swearing to himself that he will stop Aichi.

Kai heads to the Underground area to await his fateful match with Aichi. Back at home, as Aichi reviews his Shadow Paladin deck, he receives a Psy Qualia induced summon from Ren who is waiting for him at Card Shop PSY. Aichi, led by Ren's Psy Qualia summon reaches as far as outside the Card Shop when Kourin suddenly rides up throws him a helmet & tells him to come with her. Back at the Underground area, Miwa shows up with Misaki & Kamui who both implore Kai to face Aichi in a Vanguard fight and help bring him back to normal. Just as Kai informs them that that is exactly why he is here, Kourin immediately arrives with Aichi. Miwa, Kourin, Misaki & Kamui clear the area to watch the fight from a distance. Kai upsets Aichi when tells him that he still thinks he is weak & Aichi vows to prove his strength to Kai as they get ready to begin their fierce battle. Aichi is startled when he realizes Kai is going to fight him with his former Royal Paladin deck. Kai vows to show Aichi the "true power" of the deck that he threw away which rattles Aichi even more. Aichi goes first & uses his units' skills to add Blaster Dark who he refers to as his avatar from his deck to his hand. Kai has a flashback of losing his parents 4 years ago & meeting Ren from his new school & later Tetsu (after he leaves town to live with his uncle). Tetsu loses to Kai in a Cardfight & he and Ren tell Kai of Foo Fighter. They recruit Kai & they have a love of fun until one day Ren's Psy Qualia powers awakened. He beat Tetsu repeatedly claiming that he was now the "strongest fighter" ever. Ren abandoned the idea of him, Tetsu & Kai being Team Foo Fighter & has construction begin for the new Foo Fighters Headquarters where only the best fighters would be selected. Kai realizes that Ren has become obsessed with power and refuses to go along with his new plan & quickly challenges him to a card fight. The match is fierce and as Ren announces his "Final Turn" he taunts Kai but before he can claim victory his overuse of his PSY Qualia power causes him to collapse. Kai catches him in time but Ren is still fixated on how much stronger he's become. Kai quits the team & moves back home peeved about how powerless he was to stop Ren. He reminisces on how refreshing after all of this it was to meet Aichi again and of how much fun Aichi made him remember Vanguard fights to be. He also remembers how fixated Aichi had become on "getting stronger". He vows to himself that while he couldn't stop Ren, this time will be different. With stern determination to accomplish this, Kai draws & uses his units' skills to add Blaster Blade from his deck to his hand. Kai reminds Aichi that then & now his avatar is not Blaster Dark as he claims but will always be Blaster Blade. Kai faces Aichi thinking that this time he's going to teach him what true strength is & declares that he is going to stop him!

Kai rides King of Knights, Alfred to give Aichi some damage. However, on the next turn, Aichi declares "Final Turn", attacking with Phantom Blaster Dragon and Blaster Dark attacks but Kai successfully guards against both of them. Failing his Final Turn, Aichi is shocked and forced to end his turn, giving Kai the chance to show Aichi what true strength is. Kai declares "Final Turn" as he rides Alfred Early, a more powerful form of King of Knights, Alfred. Through Alfred Early's skill, Blaster Blade is Superior Called from the soul. Blaster Blade makes Aichi realize that relying on PSY Qualia isn't real power and how Aichi always wanted to have a Cardfight with Kai. The fight is called off, and Kai gives back Aichi's Royal Paladin deck.

Card Capital is holding a casual shop tournament, and Aichi, Kamui, and Morikawa enter in the senior division, while Emi competes in the junior division. Unfortunately, Morikawa has left his super-strong deck at home. Shin lends Morikawa an unmodified trial deck to use, but to his dismay it contains only one Grade 3. Can Golden Rutile go the distance?

The shop tournament continues, with Morikawa having a seemingly unstoppable series of victories and Emi's Bermuda Triangle deck dominating the junior division. Though he doesn't win, Aichi realizes that he plays Vanguard because it's fun.

The tournament finals begin and Ren delivers an egotistical speech at the beginning that angers the other teams. Team Q4 battles through the first two rounds, but coming up next is their "rivals", Team Caesar.

In the first battle of the semi-finals, Kamui faces off against Gai Usui, the "Gladiator" of Team Caesar.

The second match is between Misaki and Yuri, two female fighters with completely different playstyles. While Misaki makes her decisions based on highest probabilities and most logical outcomes, Yuri relies on her intuition to take high risks for greater rewards. The latter strategy holds true as Misaki makes a grave misplay by not going for said high risks which could have won her the match. Showing the reason why she is called the Empress, Yuri uses her instincts to draw a Stand Trigger as if she commanded her deck to allow her to do so, thus giving her enough power to defeat Misaki and take the second game. With the score tied 1-1, the last match between Kenji and Aichi will decide who will go on to the finals. As both players deal damage to each other, Aichi sets up to play Soul Saver Dragon in his next turn. However, Kenji sees through Aichi's plan and intends to put a dent in it.

Aichi battles Kenji the Emperor for the right to face Team AL4 in the finals. Can Aichi defeat his strongest opponent yet without relying on his PSY Qualia?

Although happy that Aichi woke up, Kai thought of the time when he was still young. He wanted to get Ren out of his Pysqualia self, but then Ren's image was so bad that Kai left him defeated. Now that Kai changed, he vowed to rescue Ren from his PSY Qualia addiction and is bent on winning!

Determined to turn Ren back to his former self, Kai crossrides Dragonic Overlord The End and performed Persona Blast to get Ren out of his PSY Qualia self. It didn't get Ren out of the box but got him to also crossride his own trump card (which is given by Suiko)Phantom Blaster Overlord. The period was to prepare for the worse as Phantom Blaster Overlord had the same ability as The End and could also do Persona Blast which destroyed The End. Because of this failed battle, it left Kai devastated with no hope.

The final match begins, with Kamui against Tetsu.

Although Kamui tries his hardest, Tetsu is victorious, putting Team AL4 up one game to none.

Misaki draws upon her memory power as she battles Asaka in this second-round revenge match.

Having ordered the positions of her last 16 cards thanks to the abiltys of her cards, Misaki defeats Asaka.

The final battle between Ren and Aichi begins, with Ren initially using his PSYQualia to overpower Aichi.

Ren taunts Aichi throughout their battle, trying to get him to use his PSY Qualia. Feeling angry, Aichi does and summons Blaster Dark to the surprise of everyone. However, this causes him to change his personality back into what he was before when he first uses PSY Qualia. Meanwhile, a mysterious entity possesses Rekka temporarily, informing Kourin and Suiko of an impending doom about to happen on the planet Cray and a war between the many clans which will be decided based on the outcome of Aichi and Ren's battle. The mysterious being also explains the truth of PSY Qualia. Back to the match, Kai reminds Aichi that this was not his true self which causes Aichi to overcome his dark self. As he is confused over his two selves, Ren declares 'Final Turn' and crossride Phantom Blaster Overlord and utilizing its Persona Blast.

After calling out 'Final Turn', Ren fails to defeat Aichi as Aichi miraculously draws a Heal Trigger. Aichi then realizes his true self as he summons Majesty Lord Blaster to get Ren out of his PSY Qualia addiction. Majesty Lord Blaster's skill shocked Ren as Majesty Lord Blaster could get an extra 10000 points and an extra critical by adding both Blaster Blade and Blaster Dark in the Soul. In the end, a good ending started with Phantom Blaster Overlord defeated.