No ano de 2061, o Japão tornou-se um território ocupado. Shiiba Amou vive em um mundo sombrio sob constante opressão até o dia em que ele conhece uma IA autônoma chamada "Gai". Esse encontro casual mudaria seu mundo para sempre...

Wanted as a terrorist, Amou is now on the run. Hungry and tired, Amou finds a vegetable field but is caught trying to steal the old man's crop. However, his good-natured heart wins the man's trust, and Amou finds a moment of respite...

Just when it looked like the end for Amou, Gashin, a member of the Resistance group called Yatagarasu, saves Amou and takes him to their base camp. There, Amou is recruited to join them and fight the good fight for Japan's independence.

A mysterious AMAIM attacks Yatagarasu's base camp. Tezuka and Amou team up and barely win the battle, but they are left with a devastating aftermath. Afraid of how many more deaths Amou must face if he joins them, he chooses to go his own way...

Amou decides to visit Risa's hometown in hopes that he can return her keepsake to a relative. Unfortunately, he learns that her house was torn down and her relatives were chased away by a deputy governor who isn't afraid to abuse his power.

To bring their AMAIMs into a minimally operational state, Amou and Gashin visit a nearby city to receive substitute parts from Yatagarasu's helper. Unfortunately, they get caught up in a territorial dispute between the Oceanian and Asian military...

The North American military has located the whereabouts of Ghost. Captain Brad Watt and his team are sent on a mission to capture Ghost to further their technology. Unfortunately for them, Ghost has a few more tricks up its sleeve that they're unaware of.

Amou, Gashin, and Shion finally reach Yatagarasu's HQ. They soon head out on another mission, but this time, it isn't combat-related. The members of the Resistance come together to help a Japanese family who has lost their home in the war.

Gashin bumps into Yuusei and learns that his foster brother has accomplished a great feat. He built an autonomous city for the Japanese people to safely live in. Yuusei asks Gashin to join him and live a normal life, but not everything is as it seems.

A separate Resistance group in Tohoku called Arahabaki is under attack by the Eurasian military, and is in need of help. Amou, Gashin, and Shion are sent to rescue the members of Arahabaki, and must find a way to break through their encirclement.

Moving in small groups to avoid detection and setting up temporary base camps until the new HQ is ready, the members of Yatagarasu enjoy a brief reprieve until they're able to go on larger scale missions. Unfortunately, Brad has other plans for them...

After verifying Brad's intel about Ghost, the members of Yatagarasu decide to take the fight to Ghost while also rescuing the Japanese people left behind in the war zone. Can Amou, Gashin, and Shion work together to defeat Ghost for good?

With Ghost's extraordinarly high learning capability, Amou, Gashin, and Shion's chance of winning this battle continues to drop as time goes on. The three manage to determine Ghost's weak point, but will that be enough to tip the scales in their favor?

With Ghost's AI falling into the hands of the North American military, they've come out on top in the autonomous AI race, expanding their territory in Japan. Gashin and Shion continue to fight for a brighter future, but their luck seems to be running out.

With Amou and Misuzu's return, Yatagarasu succeeds in turning the tables on the North American military. After their temporary retreat, they once again go after Yatagarasu, but they are no match for the newly upgraded Kenbu, Jogan, and Reiki.

Lead by Brad Watt, the North American military has been working hard to get Ghost combat-ready. Despite it being incomplete, Brad decides to ride Ghost to battle Alexei from the Eurasian military, and a fierce battle ensues

Worried about how closed off Amou has become after his disappearance, Gashin and Shion finally press Amou for answers. Understanding their deep care for him, Amou slowly opens up, and shares details about his time at TRYVECTA's research facility.

A Eurasian military used a pretext to create a special area where Japanese can be protected. However, the advance of the US Army now threatens the security of the site.

There's a new special mission involving the usual Yatagarasu members, but Gai, Kei, and Nayuta are kept in the dark. The members go out of their way to keep this mission top-secret, but will they be able to keep the AIs out of the loop for long?

To counter the NAC's aggressive territorial expansion in Japan, Eurasia, AFTE, and Oceania decide to team up with Yatagarasu, offering the liberation of the Hokuriku region, calling it "New Japan" and allowing full sovereignty.

To discuss the future of New Japan, Amou and Alexei travel across NAC territory. However, before the meeting could even take place, what appears to be an assassination attempt on the life of a NAC congressman causes everything to go downhill.

Unable to prove their innocence in the congressman's assassination attempt, Amou and Alexei are on the run. With Gashin too far away to come help, it's up to Shion and others to save the two before they are captured by the North American military.

Amou and Alexei are safely back with the NJCO, but their battle for their freedom came with a cost. Using that battle and the sniper incident as justification, the NAC has painted them as villains, and plans to launch a large-scale attack on New Japan.

A full-scale war has erupted between the NJCO and NAC. If the NJCO can win this war, they can finally reclaim a part of the territories of Japan. However, if they lose, they will likely lose everything. Who will come out victorious in this Boundary War?

It's the final showdown between the NJCO and NAC. With Gashin and Shion tied down, Amou and Gai must fight Brad and Ghost on their own. Despite their machine specs being inferior to Brad's AMAIM's, Amou and Gai cannot afford to lose this battle.