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. When the two teens win the brawl, Teru takes them underground, where the boys are in for the shock of their lives.

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.

Freed from her alien possession, Asuna tells Yamato and his friends what she knows, so they start searching for the hotel the aliens are using as a hideout. Meanwhile, Kota ends up drenched after saving a drowning puppy. Momoka takes him to her house since she can't just leave him in that state. While Kota tells her his life story, an agent suddenly appears in front of them and blocks their way.

Yamato and the others manage to corner Sarzant, who'd been possessing Soji, but he escapes at the last second. Kiyoka witnesses part of the confrontation. Yamato lies to her and tells her Soji wanted his advice about a stalker. Then there's Jun and Momoka, who end up being partnered as pilots. Sparks are sure to fly as they vie for dominance!

Yamato and his friends struggle against unknown armored aliens piloting their own machines. Surrounded by an electromagnetic fence, Musashi is targeted repeatedly, and the impact of the attack causes Ryugo to have flashbacks of his real mother. With their backs to the wall, Yamato learns how to deal with the Dark Hunter from an unexpected person.

Oblivion Bay is busy with preparations to launch Ixia from the surface. Amidst all the activity, Teru remembers the Day of Destruction. After losing his parents, he was saved by an alien. Yamato meets with Arshem to learn why the aliens invaded Earth and her thoughts on everything.

All Rogues are mobilized to intercept an all-out assault from a horde of Draktors. Yamato and Arshem ride into battle with them on the Musashi. Each pilot fights fiercely against the aliens in an attempt to buy the Ixia more time to succeed with their launch plan. And then Mayor Takekuma appears in Land Eye...

While the shock from the stunning revelations ripples throughout Land Eye and the battlefield, Teru receives a message from Sayaka and renews his resolve. The enemy breaks through their defensive net on the front line, and Ginta orders Jun and Momoka to escape from the Maximus. But Jun ignores him and faces off against the enemy to protect him and everyone else.

Almost a full day has passed since the battle. Building repairs in Akagicho are complete and people's memories have been restored. A new organizational structure is in place at Oblivion Bay. Meanwhile, Grieffas, incarcerated after defying Queen Crouzade's orders, escapes from his prison with his trusted associates.