Yu☆Gi☆Oh! Zexal Second

As peace returns to Heartland City following the World Duel Carnival, Astral, who has collected 50 of the 100 original Number cards at this point, receives a strange vision from within Yuma's key. Meanwhile, an emissary sent by Dumon from the Barian World, named Girag, arrives in Heartland City, and brainwashes a gang of bikers to follow under him, using the spell card Rank-Up-Magic Barian's Force. His appearance revokes a reaction from Shark's sister, Rio. As Yuma, Shark and Tori go to check up on Rio, she utters something about someone planning to take something important, reminding Yuma of the words he heard when first activated the powers of his key. Just then, Yuma receives word that the biker gang's leader, Fender, has attacked his school, demanding he brings his Numbers. Fearing Astral could be put in danger, Yuma leaves his key with Tori as he heads to the school and confronts Fender. As the duel begins, Fender instantly summons his Xyz monster, Mechquipped Angineer. As Astral senses Yuma is in danger, Utopia sends itself over to Yuma, allowing him to summon it and deal some damage. Just then, Fender activates the spell card Rank-Up-Magic Barian's Force to perform a Chaos Xyz Evolution on his Angineer, to upgrade it to the Chaos Xyz Monster Mechquipped Djinn Angeneral, and steal Utopia's Overlay Units.

Angeneral manages to destroy Utopia, despite not being a Number, causing real damage to both Yuma and Astral. Astral makes contact with Tori, asking her to bring the key to Yuma. As Kite and Shark hold off Fender's lackies, Yuma takes more damage from Fender. Tori delivers the key to Yuma, who explains the dreams he's been having to Astral. Encouraging Yuma to stand up and fight with him, Astral gives him the advice needed to bring out Utopia Ray and defeat Fender. After the duel, Kite and Shark reveal they have dealt with all of Fender's allies, while Orbital knocks Fender out, removing the control that Barian World had on him. As Yuma, Shark, and Kite decide to team up to face this new enemy, a mysterious student watches them from the shadows.

On his way to school, Yuma encounters an overly-positive, well-meaning transfer student named Ray Shadows and ends up getting dragged around by him. Meanwhile, a pro duelist named Devon Knox visits the school to have duels with the students. When Yuma expresses his interest in dueling him, Ray takes it upon himself to try and find Devon and convince him to duel. However, Devon is possessed by Girag and violenty duels against Ray to get Yuma's attention. Yuma begins a duel with him and summons out Number 34: Terror-Byte whilst Devon summons out his ace monster, Giantrainer. After using its effect damaging abilities, one of which backfires against him, Devon uses Rank-Up-Magic Barian's Force on Giantrainer to upgrade it into the Chaos Xyz monster Ultimatrainer, using its ability to test Yuma's drawing luck. Yuma manages to survive the effect and use the monster cards he was forced to discard against Devon before bringing out Utopia Ray and winning the duel, freeing Devon from the Barians' control.

After Ray nominates him, Yuma is chosen as the next class president, much to Caswell's dismay. The Student Council President, Carlyle Chesterton, who is under Girag's command, assigns Caswell as a "Special Disciplinary Commander", who begins enforcing harsh rules on the students. As Yuma decides he has had enough and confronts Carlyle, he challenges him to a duel, with Caswell as the referee, throwing in all sorts of rules which obstruct Yuma's dueling. Carlyle summons his Xyz Monster, Norito the Moral Leader, and deals some damage to Yuma, though he manages to find a workaround to Caswell's rules. As Caswell laments how he isn't class president anymore, Yuma reminds him of his true self, allowing him to throw away the role of disciplinary commander. Carlyle then uses Barian's Force to upgrade Norito into the Chaos Xyz monster, Saimon, the Great Moral Leader, but Yuma manages to bring out Utopia and win the duel. Afterwards, Yuma relinquishes his role as class president back to Caswell while Girag finds a new target to put under his control.

A manga artist named Art Stanley requests that Yuma and Shark be models for his manga, but Shark refuses. Unknown to them, Art is under the Barians' control, tailoring Shark to report his weakness to Girag. The next day, Shark discovers that Rio has gone missing and is confronted by Art, who challenges him to a duel. Art quickly summons his Xyz monster, Comics Hero King Arthur, and uses Rio as a means to stop Shark from fighting back, claiming she will become trapped forever if he is defeated. Believing Art's sketchbook may provide a hint to his weakness, Yuma and Ray set off in search for it. Meanwhile, Art forces Shark to summon out Shark Drake and deals a lot of damage before activating Barian's Force, ranking up King Arthur into the Chaos Xyz monster, Comics Hero Legend Arthur, using it to destroy Shark Drake. After some encouragement from Yuma, Sharks calls out to Rio and manages to both free her from captivity and awaken her. Shark soon regains his resolve and brings out Shark Drake Veiss to win the duel.

Rio starts attending Duel Academy, instantly becoming popular with the boys and proving embarrassing for Shark. As Rio manages to overwhelm any club offers with her amazing talent, she and the others are approached by the Flower Arrangement Club's president, Lotus Henazoe, who soons start putting everyone besides Yuma into a trance, revealing herself to be under Girag's control. As Lotus challenges Yuma to a duel, Rio decides to take her on in his place. Lotus summons her Xyz Monster, Battlecruiser Dianthus, and soon uses Barian's Force to upgrade it to the Chaos Xyz monster, Battleship Cherry Blossom, bringing Rio's life points down to 200. Rio soon summons her own Xyz monster, Zerofyne, and manages to use her cards to Lotus.

Noticing Girag's repeated failures, Dumon sends another one of his disciples, Alito, to the Duel Academy, where he ends up getting a crush on Tori. Alito tries to make various attempts to woo Tori, but all of them are inadvertently thwarted by Yuma. Wanting to prove himself, Alito challenges Yuma to a duel, quickly summoning out his Xyz monster, Battlin' Boxer Lead Yoke, and soon realizes who he is up against. Yuma summons his Xyz monster, Gauntlet Launcher, and manages to win by countering Alito's own counters. After the duel, Alito takes a shining to Yuma and declares him his rival.

When Ray makes an innocent suggestion to have a mascot girl for the Numbers club, the resulting arguments causes Tori, Cathy and the others to fall out with each other. Seeing an opportunity, Girag approaches Yuma, who is unaware of his connection to Barian World, and suggests they hold a sports duel tournament to help them make up. The tournament begins the next day, with Yuma and Shark's team pushing ahead while the team consisting of Tori and Cathy lags behind, though they manage to get over their fighting. As Girag arranges a duel between Yuma and Tori's teams, he puts Tori and Cathy under the Barian's control. With Shark going home for the day, Girag ends up getting drafted into Yuma's team, putting him in an awkward situation. Tori summons out her Xyz Monster, Fairy Cheergirl, and uses Barian's Force to upgrade it to the Chaos Xyz Monster, Dark Fairy Cheergirl. However, Yuma manages to summon Utopia and power it up with Girag's trap to win the duel, freeing the girls from the Barians' control.

As Dumon sends yet another Barian emmisary, named Mizar, to Earth, Yuma continues to be plagued with nightmares about losing Astral. Noticing Yuma's lack of energy, Haru asks Tori to take him to Roku's place, where they once again meet Kaze, who gives Yuma some spell cards from Roku. The next day, as Rio suddenly prophesises about a fearsome dragon, Yuma is confronted by Mizar, who traps him in a Sphere Field, forcing him into a duel. Determined to protect Astral, Yuma instantly summons Utopia, using one of Roku's cards to protect his overlay units from Barian's Force. To both Yuma and Astral's surprise, however, Mizar summons an Over-Hundred Number card, Number 107: Galaxy-Eyes Tachyon Dragon, resembling the dragon from Yuma's nightmares.