21世紀中期，經歷慘烈的「境界戰」後，日本遭受全球四大經濟體割據統治。熱愛機械的少年椎葉海士，生為日本人的身分使他對未來不抱希望，某天他在山中遇到了能夠自主思考的人工智慧「垓」，並為了保護朋友，而搭上人型特殊機動兵器「AMAIM」，海士與世界的命運就此轉變。

在大洋洲軍的襲擊之下逃過一劫的海士與垓踏上逃亡之路。某天，飢餓難耐的海士在深山中走進了一座小小的田地，並在那裡遇見了好心的老夫婦，靠著他們的幫助繼續前進。然而，擋在前方的是以行動統一著名的亞洲軍，海士是否能順利逃出生天呢？

遭受亞洲軍攻擊的海士與垓，被一架未曾見過的神秘AMAIM拯救，其戰鬥力之強大，轉眼間就把亞洲軍的無人機部隊全數擊倒。這架AMAIM帶領海士他們來到一個秘密營地，原來是訴求日本復權的反抗軍組織「八咫烏」的根據地。海士會加入他們嗎？悄悄襲來的黑色機體又是何方神聖？

偷襲八咫烏營地的黑色機體，竟然是殺死雅心父親的神秘無人機「鬼魂」，即使海士與雅心同心協力，仍然難以敵過鬼魂的強大實力。四處襲擊各方組織的鬼魂，背後究竟是誰在操控？八咫烏遇襲之後傷亡慘重，海士也受到了沈重的打擊，究竟他的決定會是……？

海士來到了莉莎的故鄉，想跟莉莎的親人或朋友告知她的消息。佔據此地的亞洲自由貿易協議派駐了一位新的代理執政官，而他卻利用權勢暗地裡進行不道德的勾當，並打算將魔爪伸向莉莎的朋友們。才剛經歷生離死別而大受打擊的海士，是否能夠振作起來戰鬥，保護大家呢？

一邊避開亞洲軍耳目，一邊朝反抗軍總部前進的海士和雅心，因機體受損而進城採購零件。不巧，居心叵測的大洋洲軍發動了攻勢，而進行反擊的亞洲軍，卻已無暇顧及城中居民的安危。此時一架神秘機體橫空而出，說要「處罰」大洋洲軍和亞洲軍，這架機體究竟是何方神聖？

海士與雅心和新成員史恩會合後，三人一起前往八咫烏反抗組織的總部。與此同時，北美軍在布萊德的率領之下，決定潛入亞洲軍的地盤，揪出鬼魂並將其捕獲。纏鬥中，布萊德展現了過人的指揮與戰鬥能力，但鬼魂卻以驚人的速度學習成長，究竟他們誰能勝出？

抵達八咫烏總部之後的海士、雅心與史恩，暫時放下機體與戰鬥，參與一個山中廢村的重建任務。原來八咫烏不只是個反抗作戰組織，為流離失所的日本民眾重建家園，也是復興日本的重要任務之一。他們能成功將沒水沒電的廢村，打造成適合人居的地方嗎？

有人在街上叫住了雅心，原來是被雅心父親收養，一起長大情同手足的大哥哥。離開八咫烏的他一直努力打造心目中的烏托邦，不惜與亞洲軍談判建立了專屬於日本人的自治區。他希望雅心退出八咫烏不再持槍征戰，跟他一起生活，雅心會如何決定呢？

海士、雅心和史恩接受了布連森公司的委託，前往東北救援同樣意圖解放日本的反抗組織。他們的敵人是以軍力數量取勝的歐亞軍，面對駕駛技術高超的阿列克謝，指揮能力超群的達麗雅，以及無所不在的AMAIM機體偵測器，他們是否能夠逃出生天呢？

在遷移到新的總部之前，八咫烏成員們得以度過一段稍微放鬆的時光，海士埋首於自己熱愛的機械之中，雅心和史恩則是在棋盤上徹夜大戰。某天，三人一起去市集採買物資時，偶然遇到了北美軍的布萊德上尉，這場命運的邂逅究竟會將雙方帶往什麼地方呢？

北美軍提供的情報，指出鬼魂潛藏在亞洲軍勢力範圍內的隱岐群島上，由於還有日本人居住在其中一座島嶼，因此八咫烏必須一面引開鬼魂，與它作戰，一面將落難的居民們救出。海士、雅心和史恩依照事先擬定的計畫努力將鬼魂逼進死角，究竟他們是否能打倒鬼魂呢？

在鬼魂壓倒性的速度與威力之下，海士、雅心與史恩陷入了苦戰。在他們棄而不捨的分析之下，終於找到了鬼魂的弱點，但他們能夠成功藉此將它擊倒嗎？為了讓夥伴生還脫身，海士和垓發揮了建武的全力，這項危險的任務究竟是否能夠達成？

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.

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.