A resident of Akagicho, high-schooler Yamato finds himself locked up after starting a fight. His classmate, Teru, appears and makes him a deal. In exchange for getting him out of jail, he wants Yamato to take on a job for him. Yamato and his rival, Ryugo, head for the designated spot, but are set upon by thugs Teru riled up.

Yamato, Teru, and Ryugo board the Musashi and leave the shelter. Outside, they find a fierce battlefield against the aliens. Yamato and his team plunge into the fray and rack up victories thanks to Musashi's abilities. But the aliens' combat machines undergo a shocking transformation and their enemies turn the tables on them.

Possessing Asuna's body, Arshem stalks Yamato in order to kill him, but fails when he notices her. In an attempt to maintain her cover, she lies and tells him she's in love with him. Later, Yamato and his teammates learn that one of the pilots has been assassinated.

Transfer student Reiji creeps out his classmates because he's always hanging out with cats. One day, while chasing a cat, he stumbles into Oblivion Bay. As if guided by some mysterious force, he climbs into the cockpit of the new Rogue. Then, with the cat still on board, the autopilot activates and takes off for the battlefield.

In town, Yamato and his friends see a street gang that Ryugo has a history with. When they follow the gang into their secret hideout, they're surprised by who turns out to be the gang's boss. A fierce scuffle breaks out, but Reiji's appearance interrupts it. Yamato and his friends receive orders to report to base, so they head into battle alongside Reiji and fight together for the first time.

At a summit meeting, Sayaka explains the plan to bring Ixia to the surface and head for the legendary Sanctuary. But a sophisticated operating system was required to accomplish the goal. Then they're discovered by Takumi and Kota, who snuck into Oblivion Bay to check out the new Rogues.