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Tony has to deal with the fall-out of deploying a nuke on American soil while searching for the Mandarin. The Mandarin is busy trying to unlock Maya's DNA sequence to start mass producing weaponized Extremis. Can the Mandarin be stopped while Tony is under house arrest?
Iron Man hallucinates Ho Yinsen and his son giving him clues to the Mandarin's plan. He wakes up three miles from where Gentech as, where the US military place him under arrest. Disguised as Stark, the Mandarin tells Maya the the Mandarin has cracked her Extremis PCD, and that he needs her codes to defeat him, she says she'll need proof. In New York, Stark orders Dugan and Hill to investigate Prometheus and "Borjigin" to find where the Mandarin is. In "the Trial of the Millenium", a joint session between the UN general assembly and the CSA hold court over Stark's and SHIELD's detonation of a nuclear device on American soil. Samson testifies on Stark's behalf and learns that Kooning is missing.
Meanwhile, "Stark" shows Maya footage of Shearing in confinement, testifying that the Mandarin cracked her PCD codes. She agrees to help. Dum Dum orders a Chinese Government SHIELD mole to hand over "Borjigin's" records. In Myanmar, Kooning meets with his old fellow soldier Wang Kong to ask for help in killing the Mandarin. Maya gives the Mandarin the PCD codes, he drops the illusion and calls Shearing who's readying missiles to deliver Extremis into the atmosphere.