Tony Stark sits alone, in a dark room, watching the Virtual Valerie Show. Stark turns to the day's news. The top story concerns the upcoming sale of Stark's Iron Man armor designs to the Japanese corporation, ESON. The controversial decision is followed by a profile of Stark, a billionaire recluse, now known to be the face of Iron Man. Stark dons the latest iteration of the Iron Man armor. Iron Man receives a call from a Mister Jones Jones voices his reservations about shopping Stark technology to a Japanese company. Iron Man calls Maxie Graham, a research scientist based at The Mariana Trench Undersea Research Station.
.Iron Man wishes to celebrate the sale of his technology. Graham is willing, but only if Iron Man, as Stark, meets her in Hawaii. A Dreadnought steals valuable technological information. Nicholas Fury, the former director of S.H.I.E.L.D., is called out of retirement, to rattle some cages. Fury accuses Japan, represented by Hiro Matsui, a top executive at ESON, of unleashing a virus to pirate technology. Fury calls on Stark. Fury questions Stark's decision to sell his armor technology to ESON. Stark has dinner, in Hawaii, with Graham. Their time together is interrupted by Jones.
There has been no communication with ESON since they received the final delivery from Stark. Fearing his technology may have fallen into the wrong hands, Stark journeys to Tokyo. Stark takes steps to maintain normalcy within his company. Stark meets with Keiko Takimoto, his personal escort and translator. Hideo Shinoda, the head of ESON, assures Stark that all is well, while voicing his umbrage that Stark would insinuate otherwise. Takimoto vouches for Shinoda's character. Takimoto tries to aid Stark in relaxing. Stark, and Takimoto, are attacked by an assassin.
Takimoto defends Stark, ultimately killing the assassin. Fury, leading S.H.I.E.L.D., arrives on the scene, to offer Stark protection. Stark foregoes his injection of Perpetuon, a drug that keeps him young, to regain his intellectual sharpness. Stark dons the Iron Man armor, to resolve the situation himself. Takimoto provides Iron Man with detailed maps of Tokyo. Iron Man confronts a Dreadnought. Iron Man breaches the Dreadnought's cyber defenses, discovering that the intelligence stealing virus was created by his own man, Bill Bates, at Stark International, but modified by Shinoda.
Iron Man meets with Takimoto, to pick up a drone suit of his armor. Iron Man, and the drone armor, storm the ESON building. Matsui demands that Shinoda resign as head of ESON. Matsui reveals that he framed Shinoda, as part of a scheme to return honor to Japan. Shinoda refuses to resign. Matsui orders Shinoda's murder. Iron Man enters the room. Iron Man suppresses Matsui's underlings. Matsui calls in a cadre of armored men, outfitted with Stark's technology. Iron Man calls in the drone, to even the odds. An epic battle ensues. Ultimately, Iron Man, and the drone, are triumphant.
Iron Man confronts Matsui. Matsui deploys a black box that takes control of the drone. Matsui dies in an explosion that destroys the ESON building. Iron Man pursues the runaway drone. A total systems failure takes Iron Man out of the chase. Stark regains consciousness on an island. The combination of Matsui's mysterious black box technology, coupled with Stark's own brilliant design, has inexplicably given the drone sentience. Now possessing free will, the drone sets off to find it's place in the world. Stark is rescued by S.H.I.E.L.D. Stark swears off Perpetuon, resumes his relationship with Graham, and ceases being a recluse. Periodically, Stark receives letters from the drone, a son reaching out to it's father.