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Chronologically, this arc takes place two years after Black & White arc.
- Main article: Pokémon Adventures: Volume 52
Two years after the events of Team Plasma invading the Unova Pokémon League, a new student, named Whitley, enrolls into the Pokémon School in Aspertia City. Blake, a fellow student, observes her, despite the annoyance of Hugh, another student of the school. In a quick tournament made by the new teacher, Cheren, Blake and Whitley obtain two Pokédex. In truth, Blake is actually an undercover police agent, who poses as a student to find a girl, who has a locket, which contains info on Team Plasma's newest weapon. Blake teams up with Looker, and the two go into the city, where they find a strange being, a Genesect. The two quickly discover it is controlled by Colress, the temporary leader of the renewed Team Plasma. Blake manages to capture Genesect, but Colress retreats and promises the return of Team Plasma and its leader, Ghetsis. Blake continues his mission and accompanies Whitley, who is actually a former member of Team Plasma, and a fan of N. They encounter an angry Keldeo, who knocks Whitley out. Blake saves Whitley, who wakes up and compares Blake to N. Despite the incident, two go to the Pokéstar Studios, where the two have fun and even defeat a mecha Tyranitar. After the class returns to school, a provoked Hugh attacks the girls, and finds a locket, with a chip inside. To his shock, he finds a list of the Pokémon liberated by Team Plasma, and remembers the incident involving his sister and the Purrloin he gifted her. Meanwhile, Colress has finished his project on the new Team Plasma outfits, and is ready to wage war on Unova with his "friend".
- Main article: Pokémon Adventures: Volume 52
Believing Whitley could be the Team Plasma member with the locket, Blake continues to befriend her, despite her being uncomfortable, and gives her a present. Out of nowhere, a Legendary Pokémon, a strange-looking Tornadus appears, and knocks Whitley out. Blake battles Tornadus and manages to freeze it. He finds Giallo, one of the Seven Sages, who was attacked by Tornadus, and has Looker arrest him. To comfort Whitley, Blake takes her to a concert, performed by Roxie in Virbank City. The following day, the class forms a choir to sing for a prize, with Roxie as one of the judges, and Hugh's sister observing them. They win a tour to Castelia City, with Roxie joining them. Once there, Roxie quickly discovers a man, whom she was supposed to meet at the city, whose Karrablast was "liberated". Since Team Plasma was behind that, Hugh, Roxie, Whitley and Blake go into the sewers to find these criminals, led by Bronius and Ryoku, the two Team Plasma sages. During the attack, the group splits up: Whitley and Roxie defeat the grunts, while Blake goes through the sewers. Blake comes out and discovers the three Legendary Pokémon: Thundurus, Landorus and Tornadus, all of whom have changed appearance, due to Colress' Reveal Glass. Blake battles the Legendary Pokémon and faces Ghetsis. The latter storms off on a flying ship, the Plasma Frigate, on which Blake hops on. Meanwhile, Whitley starts questioning the organization she was a part of, and contacts her mother, who reminds the importance of retrieving the locket she lost. She joins the rest of the class, who suspect she is the Team Plasma spy, and in an awkward moment, they are knocked out by her Foongy's Spore. Hugh remains unphased, and in order to learn more about Team Plasma, he takes Whitley with her. In a strange coincidence, they barely dodge the attack of the Plasma Frigate, which freezes the entire Castelia City, and knocks Hugh out. Whitley meets up with Rood, who warns her about the Colress machine and a police agent that arrests Team Plasma members. Whitley is taken captive, after Colress attempted to capture Rood, who betrayed the organization. Blake finds Whitley atop the flying ship, and upon Whitley's mention she is the Team Plasma member, he handcuffs her. Without many options left, the two storm off on Genesect to stop the ship by defeating Kyurem, whom Colress took from Zinzolin. Colress intercepts them, and has Kyurem freeze the two before they are thrown into the ocean. Just then, N, riding on Zekrom, tracks down the Light Ball.
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