Time has passed, and the members of Team TRY3 have gone their separate ways as they enter high school. Tokoha is studying abroad in France, Shion is attending Fukuhara High, and Chrono enrolls in Tokyo Metropolitan Harumi High School. However, Chrono has a hard time adjusting to his new school life. Later, while working at Card Capital 2, Chrono is challenged to a cardfight by a peculiar young man, who soundly defeats him with his Nubatama deck. Before leaving, the man reveals his name to Chrono: Kazumi Onimaru. Upon learning that Kazumi is the reigning "Under 20" Vanguard champion, Chrono decides to enter the U20 Championship.

To enter the U20 Championship, Chrono must find two other fighters and form a team with them. He recruits Taiyou but has yet to find a third member. Later at the card shop, Chrono meets an apathetic teenager named Kazuma Shouji, who also attends Harumi High School. He claims to have previously played Vanguard and requests Chrono to teach the game's rules to him. So, Chrono has a teaching fight with Kazuma, who slowly is reminded of how Vanguard is played. Despite acting nonchalant to most of Chrono's teachings, Kazuma becomes motivated when he gets the chance to stride. However, when Chrono tries to win on the following turn, Kazuma decides to quit, believing he already lost. Chrono tries to tell him to never give up until the very end and to believe in his own possibilities. He shows Kazuma that he would have gotten a heal trigger to help him, but he suddenly gets defensive upon touching his card. He then leaves, and Chrono wonders why Kazuma acted the way he did.

Learning from Chrono about Kazuma, Taiyou goes to confront Kazuma to see what kind of person he is. Despite a run-in with Kazuma's delinquent friends, Taiyou gets his chance to cardfight Kazuma. When Taiyou gains the upper hand, Kazuma almost decides to give up, which makes Chrono deduce that he has a fear of losing. However, Kazuma continues the fight and wins, much to his own surprise. Afterwards, Chrono and Taiyou decide to recruit Kazuma onto their team for the U20 Championship (despite Kazuma's refusal).

At Fukuhara High, Shion learns that the school's once-prestigious Vanguard club is past its prime and now in danger of being disbanded. Along with the club's sole remaining member, Henri Hayao, he makes a proposition to the school's board of directors; if the Vanguard club can win the U20 Championship, then the club will stay. Later, Shion and Henri have a cardfight. Noticing that Henri is playing scared, Shion helps him get over his nerves, and the two have an intense battle. After the fight, Henri remembers that they need a third member to enter the U20, and Shion knows just the person to recruit.

The one who Shion hopes to recruit to Fukuhara's Vanguard club is Rin Hashima, but doing so is not an easy task. Hayao requests for Rin to join, which she initially refuses, but he manages to catch her interest when he mentions that Mamoru Anjou will come teach the club. Later that afternoon, Rin comes to the clubroom before Mamoru does, and Shion coaxes her into playing against Hayao. While the two have their cardfight, Mamoru appears, and Shion tricks him into believing that Rin is a member of the club and she is training with Hayao. As a result, Rin reluctantly becomes an official club member.

Chrono's and Shion's teams meet and have a friendly team fight with each other.

A month has passed since Tokoha began studying abroad in France, where she is also assisting with the Vanguard Association's Paris Branch. One day, she is introduced by Jaime to a young man named Miguel Torres, a polite albeit unlucky cardfighter who aspires to be a pro in the future. Through a friendly match with him, Tokoha learns that despite Miguel's misfortune, he is indeed a strong fighter and passionate about his dream of becoming a pro. The next day, Tokoha and Miguel spend the day together when she explains how she has yet to find a goal for herself. Nonetheless, Miguel expresses how he will wholeheartedly support her. Some time later, Jaime calls Tokoha and tells her that Miguel has died.

Miguel's death has left Tokoha saddened. One day, a tour guide tells her about the history of the Eiffel Tower and how it inherits the feelings of its creator long after his death. This lights a spark in Tokoha, motivating her to have a cardfight with Jaime. Together, they realize that as long as they continue playing Vanguard, Miguel will live on in their hearts. After the battle, Tokoha decides she wants to enter the U20.

Along with a disguised Jaime, Tokoha returns to Japan to form her team for the U20. She recruits her best friend Kumi Okizaki and Satoru Enishi, who has been working at the Dragon Empire Branch, wishing to show people the appeal of Vanguard. Tokoha visits Card Capital 2 where she reunites with Chrono and Taiyou and also meets Kazuma. Wanting to know more about Kazuma, she decides to have a cardfight with him. Although Kazuma tries his hardest, Tokoha manages to win. She offers him a handshake afterwards, but Kazuma refuses it and leaves, frustrated by his lack of power as a cardfighter.

Chrono, Tokoha, and Shion enter in a U20-qualifying tournament with their respective teams. In this tournament, players are randomly paired up, and the team with the most collective victories will get a guaranteed spot into the U20. As the tournament progresses, Kazuma eventually fights Mamoru. Believing to be on the verge of losing to Mamoru, Kazuma decides to quit before the fight properly concludes, which angers Chrono. He tries to ask Kazuma about his pessimism and convince him to just try, but this leads to a small fight between the two, ending with Kazuma leaving. At the end of the tournament, Shion's team is declared the winner, and Mamoru informs Chrono about thugs who are using Vanguard to attack people.

While Tokoha's team wins a U20-qualifying tournament, Kazuma calls Chrono and tells him that he is quitting the team. Chrono goes to confront Kazuma about this, but he ends up getting captured by a gang who mistake him for Kazuma. The real Kazuma appears and challenges the gang's leader for Chrono's freedom. With inspiring words from Chrono, Kazuma manages to win, and the police (called in by Taiyou) arrive and arrest the gang.

Chrono's team, Striders, enters a U20-qualifying tournament held at the first Card Capital shop; this is their last chance to qualify for the U20. However, because Kazuma has not shown up yet, Chrono and Taiyou must fight their way through the tournament by themselves. Striders eventually make it to the grand finals, where they face Team Trinity Dragon. In the first game, Taiyou loses to Karl. Then, Misaki tells Chrono that if Kazuma does not appear within ten minutes, then Striders will lose by default. Thankfully, Kazuma appears at the last possible second and fights Kei in the second game.

Kazuma defeats Kei, which means that the final conclusive game will be between Chrono and Tsuneto. Chrono struggles against Tsuneto, since Team Trinity Dragon has significantly improved their skills through training at Card Capital #1. Nonetheless, Chrono defeats Tsuneto, thus winning the tournament and qualifying his team to the U20.

Before the U20 starts, Chrono, Tokoha, and Shion have their own "send-off parties" with their respective teams. Jaime Flowers relax at a spa resort, the Fukuhara Vanguard Club has lunch on a cruise ship, and Striders engage in a curry-eating contest. At the end of the day, they are all treated to a fireworks show prepared by Shion. Then, the U20 Championship begins, where the other qualified teams are introduced and Kazuma is shocked to see Onimaru...

The U20 begins with its first stage, the Cray Scramble, in which fighters are scattered across a virtual field resembling the planet Cray. They will have to search for and battle other fighters to gain points, and the first sixteen teams to get fifty points will qualify for the second stage. Defeated fighters are temporarily eliminated but can be brought back if a fellow team member gets a win. As the first stage progresses, Chrono meets Team New Nippon, a group who admires and models itself after Team Nippon. He fights the leader of New Nippon, Arata Nishizawa, and defeats him. When the first day ends, everyone is stunned when they learn that Onimaru's Team Diffrider has already advanced with Onimaru beating Shion and Tokoha in the process.

On the second day of the first stage, Kazuma faces Makoto Asada of Team New Nippon. While fighting, Makoto reminisces about the time when he first met Arata and how Team New Nippon was formed. Ultimately, Makoto defeats Kazuma. Just as Taiyou learns of this news, he comes across Tokoha.

Tokoha and Taiyou cardfight each other, with Taiyou wanting to win to get Kazuma back in the tournament. After a long and arduous battle, Taiyou manages to win, thus bringing Kazuma back into the fray and Tokoha once again knocked out.

Enishi cardfights Kamui, who applies an enormous amount of pressure on him. In the middle of the battle, Enishi learns that Kumi has also lost, causing him to worry even more. However, Enishi withstands Kamui's attacks and defeats him, thus allowing Tokoha and Kumi to return to the tournament.

The second day of the U20 first stage ends. As all the teams return to their homes, Chrono meets Team New Nippon and has dinner with them. Meanwhile, Rin decides that she is fed up with being on the team. She challenges Shion to a cardfight on top of a skyscraper; if she wins, then she will quit. At first frustrated by Shion's reasons for wanting to enter the U20 in the first place, Rin rekindles her own fighting spirit through this fight. Afterwards, Rin decides to stay with the team.

The third day of the U20 begins, where Henri gets starstruck when he faces Am Chouno. Despite the disadvantage her Granblue deck has against Henri's, Am defeats and then gives him a Rummy Labyrinth keychain. Afterwards, she, Luna, and Saya get reacquainted with Tokoha, Kumi, and Enishi.

The third day progresses with only eight teams remaining. Kazuma finds himself playing against Luna Yumizuki, who wants to make him smile through this fight. Though initially pressured by Luna, Kazuma defeats her and becomes a fan of hers. Meanwhile, Chrono loses to Nagisa, who mentions that Kamui entered the U20 because of Kouji. Chrono tries to ask Kamui about this but is unable to get an answer from him.

A sudden power outage occurs, which was caused by Onimaru and his team. Amidst the confusion, Onimaru tries to sneak his way into the field but is halted by Chrono and Kouji. Onimaru and Kouji have a cardfight with Chrono observing them. However, when the power comes back on, the fight is called off. Later, as the first stage resumes as normal, Onimaru returns to his original objective: a portal that Noa Hoshizaki of Team Nippon had accidentally stumbled upon. Inside the portal, Onimaru performs a Different World Ride, making Noa become possessed by Star-Vader, Chaos Breaker Dragon.

Near the end of the first stage's third day, Tokoha fights and defeats her rival Rin, who has always been like a wall for her. With this victory, Tokoha's team advances to the second stage, which leaves only two spots remaining.

The fourth day of the first stage ensues with Shion cardfighting Taiyou. Despite Taiyou learning about Shion's style from Chrono, Shion manages to win, thus gaining enough points for his team to advance to the second stage. Elsewhere, Chrono comes across Noa...

All eyes turn to the cardfight between Chrono and Noa; whoever wins will earn his team the last spot to the second stage. As the fight goes on, Chrono slowly realizes that Noa is not acting like his usual self and is reminded of the time when he fought Onimaru. Despite overbearing pressure from Noa, Chrono makes a comeback victory, thus allowing Team Striders to advance to the second stage.

Chrono is invited to the first Card Capital shop where he is introduced to Aichi Sendou. After Aichi gets reacquainted with his old friends, he and Kamui take Chrono back to Card Capital 2 to meet with Kouji. Along the way, Chrono gets to learn more about Aichi, who later gives him a new Gear Chronicle card that has a hefty activation cost. When the trio reaches the shop, Kouji is not present. To pass the time till he arrives, Chrono and Aichi decide to have a cardfight.

Chrono and Aichi engage in a heated cardfight. Although Chrono tries his best to fulfill the conditions of the new card he got from Aichi, he is defeated before getting the chance to use it. Later, when Kouji and Kai arrive, they intend to leave with Aichi and Kamui. Chrono wants to come along, but Kouji decides to test him to see if he is worthy enough.

To see if Chrono is strong enough for the challenges to come, Kouji cardfights him. Chrono manages to use the card given to him by Aichi, Beyond Order Dragon, to its fullest potential and defeat Kouji with it. With Chrono proving himself, he goes with Kouji and the others to see someone who knows about Team Diffrider: Nome Tatsunagi.

Chrono and the others meet and consult with Nome Tatsunagi, who tells them what has been going on. According to him, there are units who come from Planet Cray and possess fighters via a method called "Different World Ride", or "Diffride" for short. However, in the case of Onimaru and Noa, they have been possessed by evil units.

The U20 continues into its second stage. Dubbed the Castle Royale, fighters will battle each other in a five-tiered castle area. The first four teams to reach the top of the castle and have the highest amount of points will then advance to the final stage. Furthermore, unlike the first stage, once a fighter loses a match, they will be eliminated with no chance of returning into battle. As the Castle Royale goes underway, Taiyou fights and loses to Team Diffrider's Verno Farenheart.

Tokoha faces Team Diffrider's Saori Fuchidaka, who is possessed by Flare Trooper, Dumjid and thinks poorly of humans. Before being defeated, Tokoha is drawn into an image of a battlefield on the Planet Cray, showing her the horror of death. This reminds her of a similar event when she met Miguel...

During Tokoha's battle against Saori, Enishi challenges Onimaru, who had already beaten Am, Luna, and Kumi while trampling on their feelings of Vanguard being fun. Following his friend Miguel's death, Onimaru has lost faith in humanity, but he changes his mind when Enishi almost pushes him towards defeat. However, using the Domination effect to turn Enishi's rear-guards against him, Onimaru wins. With that, Team Jaime Flowers is eliminated from the U20.

The first day of the second stage nears its end as Chrono fights Saori. Thinking that he has this battle won, Saori is shocked when he sees Chrono render him unable to guard against his attack and make a comeback victory. Afterwards, Chrono rushes to Kazuma, who is currently fighting Onimaru.

Kazuma and Onimaru clash in a battle between step-brothers. When they were younger, they lived and played Vanguard happily together. However, due to Kazuma's mother marrying into the Onimaru family, he was shunned, looked down upon, and eventually exiled from the family. Furthermore, Kazuma could never beat Onimaru in a cardfight. Although Kazuma has matured since then, he is still unable to beat Onimaru. As Onimaru walks away disappointed in Kazuma, he tries to rush towards him but is stopped by Chrono, who now learns of the two's brother relationship.

Although the first day of the U20's second stage ends, Chrono challenges Onimaru to a cardfight. During the battle, Chrono exposes Onimaru as being possessed by a unit from Cray: Stealth Dragon, Shiranui. He asks about Onimaru's motives, and he responds it is to be liberated from destiny. As he puts it, Vanguard is what connects the planets Earth and Cray, and the fights that occur on Earth affect Cray, which Onimaru cannot tolerate anymore. Not wanting his future to be decided by a greater power, Onimaru's goal is to sever the bond between Earth and Cray by destroying Vanguard. Onimaru defeats Chrono and takes his leave.

The second day of the second stage begins. Although the Fukuhara club decided to avoid the stronger teams including Chrono's, Henri cardfights Verno. Upon learning this, Shion rushes over to Henri, who tells him to play Vanguard the way he wants and not for Fukuhara's best interest. After Henri shockingly defeats Verno, Shion catches up to Chrono and challenges him.

In spite of the high stakes, Chrono and Shion thoroughly enjoy their cardfight which reminds everyone of how fun Vanguard can be.

The U20's second stage ends with Team Diffrider, Striders, and the Fukuhara Club advancing to the final stage. Additionally, there will be a repechage in which a disqualified team will earn the chance to enter the final stage alongside the other three. Afterwards, Jaime takes Chrono, Shion, Tokoha, and all of their friends to a deserted island where he reveals the true intentions of Team Diffrider. Later, everyone prepares dinner while further bonding with their teammates.

Team Jaime Flowers fight Rummy Labyrinth with Saya in the repechage. Afterwards, the matchups for the U20's final stage are decided, with Diffrider facing the Fukuhara Club and Jaime Flowers against Striders.

Chrono and Taiyo are looking back on the trajectory of the battle at U20 for the final stage that is about to begin. Kazuma joins there, and the Striders solidify their determination before the final battle.