21世纪中期，经历惨烈的“境界战”后，日本遭受全球四大经济体割据统治。热爱机械的少年椎叶海士，生为日本人的身份使他对未来不抱希望，某天他在山中遇到了能够自主思考的人工智慧“垓”，并为了保护朋友，而搭上人型特殊机动兵器“AMAIM”，海士与世界的命运就此转变。

在大洋洲军的袭击之下逃过一劫的海士与垓踏上逃亡之路。某天，饥饿难耐的海士在深山中走进了一座小小的田地，并在那里遇见了好心的老夫妇，靠着他们的帮助继续前进。然而，挡在前方的是以行动统一著名的亚洲军，海士是否能顺利逃出生天呢？

遭受亚洲军攻击的海士与垓，被一架未曾见过的神秘AMAIM拯救，其战斗力之强大，转眼间就把亚洲军的无人机部队全数击倒。这架AMAIM带领海士他们来到一个秘密营地，原来是诉求日本复权的反抗军组织“八咫乌”的根据地。海士会加入他们吗？悄悄袭来的黑色机体又是何方神圣？

偷袭八咫乌营地的黑色机体，竟然是杀死雅心父亲的神秘无人机“鬼魂”，即使海士与雅心同心协力，仍然难以敌过鬼魂的强大实力。四处袭击各方组织的鬼魂，背后究竟是谁在操控？八咫乌遇袭之后伤亡惨重，海士也受到了沈重的打击，究竟他的决定会是……？

海士来到了莉莎的故乡，想跟莉莎的亲人或朋友告知她的消息。占据此地的亚洲自由贸易协议派驻了一位新的代理执政官，而他却利用权势暗地里进行不道德的勾当，并打算将魔爪伸向莉莎的朋友们。才刚经历生离死别而大受打击的海士，是否能够振作起来战斗，保护大家呢？

一边避开亚洲军耳目，一边朝反抗军总部前进的海士和雅心，因机体受损而进城采购零件。不巧，居心叵测的大洋洲军发动了攻势，而进行反击的亚洲军，却已无暇顾及城中居民的安危。此时一架神秘机体横空而出，说要“处罚”大洋洲军和亚洲军，这架机体究竟是何方神圣？

海士与雅心和新成员史恩会合后，三人一起前往八咫乌反抗组织的总部。与此同时，北美军在布莱德的率领之下，决定潜入亚洲军的地盘，揪出鬼魂并将其捕获。缠斗中，布莱德展现了过人的指挥与战斗能力，但鬼魂却以惊人的速度学习成长，究竟他们谁能胜出？

抵达八咫乌总部之后的海士、雅心与史恩，暂时放下机体与战斗，参与一个山中废村的重建任务。原来八咫乌不只是个反抗作战组织，为流离失所的日本民众重建家园，也是复兴日本的重要任务之一。他们能成功将没水没电的废村，打造成适合人居的地方吗？

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 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.