Sometime after the events of The Avengers, a haunted Tony Stark has obsessively built several Iron Man suits in his mansion. This causes friction with his girlfriend, new Stark Industries chief Pepper Potts. In a flashback to New Year's Eve 1999, Tony, with his scientist paramour Maya Hansen, arrogantly avoids crippled scientist Aldrich Killian, who wants Tony's backing in his endeavorAdvanced Idea Mechanics (AIM).
In present-day America, a string of bombings by terrorist the Mandarin has left intelligence agencies bewildered at the lack of forensic evidence. When Stark Industries security chief Happy Hogan is caught in one such attack, Stark overcomes his stupor and issues a televised threat to the Mandarin, who responds by destroying Tony's home with helicopter gunships. Pepper and Maya, who had come to warn Tony, survive the attack. Tony then finds himself in rural Tennessee after his artificial intelligence JARVISfollows a flight plan from Tony's investigation into the Mandarin. Tony's experimental armor lacks sufficient power to return to California, and the world believes him dead.
Teaming with Harley, a precocious 10-year-old boy, Tony investigates the remains of a local explosion bearing the hallmarks of a Mandarin attack. He discovers the explosions were triggered by soldiers from the Extremis program, an experimental treatment intended to allow its users to recover from crippling injuries. However, if a user's body cannot properly metabolize Extremis, the user heats up and explodes. After veterans started growing unstable and exploding, their deaths were used to cover up Extremis' flaws by manufacturing a terrorist plot. Tony witnesses Extremis firsthand when Mandarin agents Ellen Brandt and Eric Savinattack him.
With Harley's help, Tony traces the Mandarin to Miami. Stark infiltrates the headquarters using a variety of home-made weapons. Inside he discovers the Mandarin is actually a British actor named Trevor Slattery, who is oblivious to the acts the Mandarin has carried out. The Mandarin is a creation of Killian, who appropriated Maya's Extremis research as a cure for his own disability and expanded the program to include injured war veterans. Killian reveals he is the true Mandarin and has kidnapped Pepper and subjected her to Extremis, intending to infuse her with superhuman abilities and turn her against Tony as leverage to gain Tony's aid in fixing Extremis's flaws.
Killian has also manipulated American intelligence agencies regarding the Mandarin's location, luring James Rhodes — the former War Machine, now rebranded as the Iron Patriot — into a trap to steal the armor. Tony escapes his captivity and reunites with James, discovering that Killian intends to attack President Ellis aboard Air Force One. Remotely controlling his Iron Man armor, Tony saves the surviving passengers and crew but cannot stop Killian from abducting Ellis. They trace Killian to an impounded oil drilling platform where Killian intends to kill Ellis on live television. The Vice President will become a puppet leader, following Killian's orders in exchange for Extremis to cure a little girl's disability.
On the platform, Tony goes to save Pepper, and James saves the President. Tony summons each of his Iron Man suits, controlled remotely by JARVIS, to provide air support. James secures the President and leads him to safety, while Tony discovers Pepper has survived the Extremis procedure. However, before he can save her, a rig collapses around them and she falls to her apparent death. Tony is forced into confronting Killian and traps him in an Iron Man suit that self-destructs, but fails to kill him. Pepper, whose Extremis powers allowed her to survive her fall, intervenes and finishes Killian once and for all.
After the battle, Tony orders JARVIS to destroy each Iron Man suit remotely, as a sign of his intention to devote more time to Pepper. The Vice President and Slattery are arrested. Pepper undergoes surgery to remove Extremis, and Tony to remove the shrapnel embedded near his heart. He pitches his obsolete chest arc reactor into the sea, musing he will always be Iron Man, even without his armor.
In a post-credits scene, it is revealed that Stark has been recounting his experiences to Dr. Bruce Banner, who awakens, having fallen asleep at the beginning of Tony's story.
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