Tokyo, 2014. An ordinary high schooler, Natsume Akira, meets with a road accident. When we wakes up next, it’s 2030, and he finds himself aboard a smuggling vessel in the Tokyo Bay. What’s more, his body is all mechanical, with only his brain remaining the way it was.

Shiga practically forces Akira to join the Tokyo MPD’s Anti Ex-Arm Squad. Akira’s all at sea, but he and Rokuoin Chikage go on patrol around Tokyo, which is in full decay now, and meets a girl named Koharu. Meanwhile, several terrorist bombings happen in the city, and when Akira learns that Koharu might be in danger, he works with the rest of his squad and captures the culprits. Watching Akira’s tireless efforts during the investigation leads the rest of the squad to accept him as one of their own.

The Counter EX-ARM Squad heads to the Yokosuka Special Economic Zone to retrieve the EX-ARM held by the former president of the Mwange Republic, Jason Mraw, who has taken exile in Japan. But his android, Elmira, shows up in a Bibot and uses an ability resembling that of an EX-ARM to stop them. Her attacks make her targets vanish, and Akira and the squad are powerless against it. That’s when additional equipment sent by Shiga arrives at the scene.

Akira connects to Iriya Heavy Industries’ combat exoframe, Ogre. He uses it freely despite it being his first time, and attacks Elmira’s Bibot. When Elmira mentions that fighting is their only purpose in life, Akira regains part of his memories and goes berserk in the Ogre, taking out Elmira and Mraw. It takes Minami and Alma to bring him back to senses.

Akira conjures up a virtual space where Minami is a classmate, Alma a transfer student, and the rest of the Squad is also involved in a high school setting. The Squad attempts to revive Akira’s memories by stimulating his subconscience, and are secretly joined by Ygg. Akira ends up facing off against “Beta,” an individual identical to himself possessing EX-ARM Number 11, which caused great destruction in Tokyo. He comes to believe that Beta is the root cause of everything.

An EX-ARM auction is organized by an individual who calls themselves “Auctioneer.” Criminal groups from all across the world flock to the Megafloat hoping to get their hands on them. The Counter Squad is asked by the government to investigate the auction undercover as the bodyguards of Jinkokusha, the leading group in the Japanese underworld. They are immediately dragged into an inter-group conflict, and Akira loses consciousness in combat. When he wakes up, he’s greeted by Auctioneer.

Minami learns that Jinkokusha was involved in the incident that killed her family members and goes to see Al Jarde, seeking the whole truth. Al Jarde had also lost his family to them and was waiting for a chance to take revenge. Minami, who’s there as a Jinkokusha bodyguard, has to face off against him, but he has with him Alma, whose AI has been rewritten, and Soma, Minami’s little brother who was supposed to be dead. Meanwhile, Kondo and Ygg, who has materialized in physical form, also find themselves in battle. As chaos heightens all over the place, Beta sends a message.

Beta takes Jinkokusha hostage and lures the Counter Squad into the stadium, and they’re joined by Al Jarde, Nguyen, and Auctioneer with EX-ARM Number 11. As they all seek to carry out their own plans, Akira breaks into Beta’s network and learns that he too is Number 00. After freeing Jinkokusha, Akira returns to the stadium, but that’s when a squadron of JDF multipods make their landing and attack everything in sight, including the Counter Squad.

Ogre shows off its overwhelming strength, but Beta takes control of every machine he can lay hands on to fight it. Alma shows a glimpse of a will that no android could have during her battle with Soma. Meanwhile, Kondo and the others safely escort Jinkokusha out of the island. As the battle between Ogre and Beta grows ever fiercer, Auctioneer reveals that he’s Akira’s brother and tells the story of how Alpha and Beta had come to be.

The only way to beat the giant Beta is via direct attack to the brain, forcing Ogre into a very perilous situation. Auctioneer risks his life to locate the brain, and Ogre uses Number 11 to take it out and defeat Beta. He reunites with the Squad and celebrates, but his joy would be short-lived.

Akira has returned alive after defeating Beta, but soon Tokyo is targeted by a large-scale hacking attack. He dives into the network along with Ygg’s clones to figure out the cause, and fights the enemies within, but in the meantime the hacking spreads to the entire world. It takes over military bases and fires a volley of ICBMs, seeking to destroy the entire world. In order to save humanity, Akira makes a decision born of love.