You thought your neighbors were bad...but at least they're not aliens trying to kill you! Destroy thy Neighbor! A gate to another dimension has burst open, and invincible monsters called Neighbors invade Earth. Osamu Mikumo may not be the best amon...
After school, Ai Kitora appears to ensure Osamu doesn't run away from his punishment. Yūma argues with Kitora about her grudge against Osamu and her obsession with rankings. As they're bickering, they see an irregular gate open above the city, and a new Trion Soldier appears in the sky, dropping bombs on Mikado City.
Kitora strikes a fatal blow to the Ilgar attacking Mikado City, but activates its self-destruct ability. Without being seen, Yūma creates a chain and drags the Ilgar into the river just before it explodes. Yūma causes Kitora to reflect on these events and her opinion of Osamu. At Headquarters, Yūichi Jin enters a meeting with the Administration and Osamu. They discuss Osamu's unauthorized use of his Trigger and the appearance of the irregular gates. Jin is given the assignment to investigate and asks for the responsibility of Osamu in exchange. Just before he leaves, Osamu is questioned by Shūji Miwa about the recent battles involving Yūma. Both Miwa and the Commander-in-Chief are suspicious of Osamu's potential contact with an unknown Neighbor.
After Osamu is expelled from Border, Jin meets him, and is introduced to Yūma, discovering Yūma is a Neighbor. Yūma then reveals that the irregular gates were being caused by a Neighbor, and Border makes an effort to find and destroy every last one of them. By Yūma's request, Osamu is given the credit for the information. Meanwhile Miwa Squad investigates Osamu, but Jin asks them not to. Later, while waiting for Osamu, Yūma meets Chika Amatori, a mysterious girl who seems capable of feeling the presence of Neighbors. When a danger alarm sounds, Chika runs to the danger zone, and Yūma follows her, saving her from a trion soldier. Osamu, who became a B-Rank Agent, defeats the trion soldier. Yūma then learns Chika's secret, and that she and Osamu already know each other, to his surprise.
Osamu explains to Yūma and Replica that Chika attracts Neighbors and is also able to feel their presence. After moving to Yumite District Station to talk more reservedly, Yūma explains to them why Neighbors invade the city, and Replica offers to measure her Trion, while Osamu and Yūma talk. Miwa and Yōsuke Yoneya of Miwa Squad see Chika with Replica and assume she's a Neighbor, but Yūma states that he is the real Neighbor and combat ensues between him and Miwa Squad
As Yūma and Miwa Squad's battle is prolonged, Miwa Squad seems to be getting the upper hand, when Tōru Narasaka manages to shoot his arm, and Miwa weighs him down with his projectiles. However, Yūma copies Miwa's projectiles and uses them about him and Yoneya, effectively incapacitating them. Jin, who had been watching the battle, approaches them, along with Narasaka and Shōhei Kodera. He explains to Miwa that Yūma's Trigger is actually a Black Trigger. After Miwa bails out, Jin and Osamu go to the HQ, while Osamu asks Yūma and Chika to stay together. In the end, Jin is ordered to kill Yūma and capture his Trigger, but says he can't.
When asked why he can't kill Yūma, Jin explains Masamune Kido can't order him directly, as he's part of Tamakoma Branch and thus works under Takumi Rindō instead. Eizō Netsuki and Motokichi Kinuta are annoyed by that, as it's the same thing in the end, but Mr. Kido tells Mr. Rindō to give Jin the same order.
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He complies, however, he gives Jin the permission to go with whatever approach he wants, bothering the other admins. Before Jin and Osamu leave, Katsumi Karasawa asks Osamu what is Yūma's goal, and he explains he was searching for his father's friend on Border. When Osamu is asked by Karasawa what is Yūma's name, Kido, Shinoda and Rindō are shocked to discover who his father is. With that information in hand, Shinoda is vocal on his opinion against taking Yūma's Trigger, but, as suggested by Karasawa, Kido decides to wait until the Best Teams on Border are back from an expedition to send them after the Black Trigger.
Osamu, Yūma and Chika are introduced to are introduced to Kirie Konami, Kyōsuke Karasuma and Reiji Kizaki, who are going to be their masters from now on. Meanwhile, Border's Upper Echelons welcome back the teams that were on an Away Mission, who are finally back.
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