EX-ARM is set in a near-future Tokyo where superweapons known as EX-ARMs have become objects of violent pursuit. In 2014, Akira Natsume, a high school student who hates machines, is hit by a truck. After a 16-year-long coma, he awakens in 2030 to find himself inside a machine interface. As he struggles to adjust, police officer Minami Uezono and her android partner Alma reveal that his brain has been preserved inside an EX-ARM, a weapon of mass destruction. Their explanation comes during a dangerous operation at Tokyo Harbor, where the three are trapped aboard an enemy smuggler ship and forced to rely on ingenuity and combat skills to survive.
Akira is initially reluctant to fight, but memories of his brother's words from before the accident push him to act. By possessing Alma's body, he uses martial arts against their attackers, and when Alma plugs him into one of the ship's ports, he discovers the devastating potential of his EX-ARM by hacking the vessel and taking control of it. After returning safely to land, Akira meets the rest of the EX-ARM Countermeasure Prevention Team, a police division dedicated to limiting the damage caused by EX-ARMs. As he witnesses the atrocities committed by those who seek these weapons, he decides to join Minami, Alma, and the team to stop the terror they unleash.
