During Secret Invasion, the Skrulls uploaded a virus that destroyed all Starktech - including the conduit that linked Tony to his Extremis suit. his suit became harder to control, Stark uploaded a virus to destroy all records of the Super-Hero Registration Act, and thus prevented new H.A.M.M.E.R. Director Norman Osborn from learning the identities of his fellow heroes. The only copy remaining was in Stark's brain, which he tried to delete bit by bit while on the run in one of his extra armors. As Osborn had him hunted as a fugitive, Stark traveled worldwide on his quest to wipe out his mental database, going so far as to inflict brain damage on himself while revisiting scenes and people important to the Iron Man mythos. Osborn, wearing his Iron Patriot armor, caught up to the debilitated Stark, wearing his Mark-1 armor, and beat him savagely. Pepper Potts is able to broadcasts the beating worldwide, costing Osborn credibility and giving Stark public sympathy. Stark goes into a vegetative state, having previously granted Donald Blake (alter ego of the Norse-god superhero Thor) power of attorney. Stark ends up in Broxton, Oklahoma while people gather to determine Stark's fate.
Detailed Plot Summary
Part One: Shipbreaking
During the events of Secret Invasion, the Skrulls had uploaded a destructive virus that targeted all Stark technology, from cellphones to the Extremis armor. As a result, the name Stark became synonymous for failure, and Iron Man himself was held responsible for the Skrull infiltration. Post-Secret Invasion, Tony Stark and his second-in-command - Maria Hill - have both been stripped of their ranks in S.H.I.E.L.D., as the global peacekeeping force is replaced by the newly-formed H.A.M.M.E.R. And the new head of H.A.M.M.E.R. is none other than Norman Osborn himself - director of the Thunderbolts program and former supervillain the Green Goblin.
At the start of the story, Maria Hill is seen packing up her belongings and vacating her office. Her dismissal is met by snickers from her former colleagues, who are now H.A.M.M.E.R. employees (particularly a chubby agent named Walsh). At the same time, Tony is attempting to help with repairs from the Skrull invasion, but his inability to pilot the Extremis suit causes him to drop some debris, endangering the lives of the construction crew on-site. The construction people angrily tell him to leave, and we next see him with Pepper Potts as he begins upgrading the repulsor tech in her chest that he put in during the events of Five Nightmares. Later, Tony is seen meeting with Norman Osborn, who asks him about the Superhuman Registration Database. Tony Stark promptly tells him that he can't just access it at his leisure, and that it requires warrants, probable cause, and a federal judge to draw up records.
Tony and Maria are then subject to a strip-search by H.A.M.M.E.R. personnel before they're able to leave the Helicarrier. Meanwhile, Osborn can be seen in his office, trying to access the Superhuman Registration Database to learn the identities of superheroes, only to find that all of his queries display no results. He gets angry and hurls his computer aside. Victoria Hand and a H.A.M.M.E.R. agent come into his office to inform him that Stark left behind a virus.
In the final scene of the issue, Tony, Maria, and Pepper are in Funtime Inc., eating Chinese takeout. Tony explains that he left behind the virus - but that it would only be triggered if Osborn was trying to access a phony database he set up (which means that Osborn was illegally accessing records). Then, Tony also explains how Extremis changed his brain into a computer, and reveals that he has hidden away the Superhuman Registration Database inside his own head.
Part Two: Godspeed
Tony Stark is hooked up to a repulsor-powered station at Funtime Inc. He explains that his mind evolved to a hard drive as a result of Extremis, and says that there's all sorts of technology inside his brain that Osborn would want (e.g. how-tos for the Iron Man, Repulsor tech, personnel files for S.H.I.E.L.D. personnel). He then explains how the repulsor-powered terminal he's hooked up to allows him to access his brain directly, much in the same manner as an external hard drive. As long as he's hooked up to a repulsor-powered terminal station, he can delete everything inside his head, one brain cell at a time. This is to protect all of that information from Osborn, but unfortunately it also deletes Tony Stark himself. Memory, personality, and reflexes will all be deleted until Stark hits brain death.
Maria Hill gets angry at Stark's proposal and tells him that it's too drastic a measure. When Tony disagrees, Maria offers him a gun instead and asks him why he doesn't just shoot himself then. Tony then explains that it's not guaranteed that all of his brain will be destroyed by a bullet, and when Maria leaves angrily - refusing to take any part in it - he tricks her into activating her sequence. To delete his mind, Tony Stark split the sequence among three people (himself, Maria, and Pepper), and he manages to get Maria to activate hers by disguising it as a security pad. Basically, Maria couldn't leave the room without activating her part.
At the Chelsea Piers H.A.M.M.E.R. base, a H.A.M.M.E.R. agent informs Osborn that they've found Maria Hill. When Maria enters her apartment at Georgetown, Washington, she gets ambushed by H.A.M.M.E.R. operatives. After a brief struggle, she surrenders, and is promptly knocked out by one of the operatives. She awakes later to find herself in a H.A.M.M.E.R. craft. As one of the operatives tries to kill her, she knocks him out and attacks the craft's pilot. They crash-land into water and Maria escapes.
Back at Funtime, Pepper enters her portion of the sequence as Tony explains that he wanted the two people he trusted the most by his side when he made decisions like these. As the terminal begins deleting his brain, Tony experiences some minor pain. He then tells Pepper that he's abdicated his role of CEO to her and that there are papers in Long Island that need to be signed. He tells Pepper that Stark Industries needs to shut down.
At Thunderbolts Mountain, Osborn has called a press conference and announces that Tony Stark and Maria Hill had actionable intelligence suggesting that the Skrull invasion was imminent. He announces that the two of them were willing to negotiate for the Earth's safety (which is all lies). He then states that he wants both of them to turn themselves in immediately for questioning. Back at Funtime, Maria returns to Tony after her ordeal as he's fixing up his Renaissance Armor (Model 17, the one used during Heroes Return).
The issue ends with Pepper at Long Island, signing papers.
Part Three: No Future
At Osborn's press conference, he answers questions, stating that Tony Stark fled arrest and unleashed the virus that damaged H.A.M.M.E.R. systems, and that H.A.M.M.E.R. is repurposing the Iron Man technology for government use. Back at Long Island, a Stark employee details how Stark Industries is down to a skeleton crew and that H.A.M.M.E.R. has seized Stark assets and equipment. At Funtime, Tony tells Maria that she needs to go to Austin, Texas, to a Stark subsidiary called Futurepharm. He gives her a jump drive, telling her to plug it into any terminal at Futurepharm, which will lead her to a hard drive that she needs to take and give to Captain America (then Bucky Barnes).
Tony then explains how he has to run around the world to all his different armories. Only the repulsor technology in either the Iron Man armors or his armories can delete his brain, and whenever these are activated it will leave behind a signature, so he has to run from one to the next. He shows her all of the suits that he has stored in Funtime. Maria and Tony then sleep with one another. At Long Island, Pepper is watching a broadcast of Victoria Hand saying that Stark has to turn himself in tomorrow morning - or he'll be considered a fugitive. Pepper then secretly finds a hidden entrance in Tony's office, which leads her to find a mysterious armor clearly designed for a female user.
The next morning, Tony fails to turn himself in, prompting Osborn to issue a warrant for the arrest of Tony Stark on the charges of crimes against humanity and treason against Earth. He then announces that H.A.M.M.E.R agents are raiding multiple branches of Stark Industries and seizing all of his assets that might aid Tony in his run. Stark offices in Chicago, L.A., Rome, Berlin, Hong Kong, Seattle, and Manhattan are all hit. At the Manhattan office, H.A.M.M.E.R. personnel search for Pepper, but they don't know that she has already don the armor and fled.
Back at Funtime, Maria awakens to find that Tony has already left. She finds a note left by him, telling her to activate the explosives that he has rigged all across his Iron Man suits in Funtime. She activates the explosives and flees.
Part Four: Breach
Pepper is flying in her new armor, and the suit's J.A.R.V.I.S. A.I. is activated. The A.I. explains that the suit Pepper is wearing is called the Mark 1616, and that J.A.R.V.I.S. is the interface that bridges her with the armor. J.A.R.V.I.S. also explains that the repulsor in Pepper's chest provides the power to the armor, and that she is the suit's perfect pilot.
In Los Angeles, Henry Hellrung (formerly the superhero Anthem) is at an Alcoholics Anonymous meeting as a sponsor. He then sees Tony, who has shaved his head and famous mustache off. Henry tries to convince Stark to turn himself in, saying that he's too high-profile to disappear, but Tony Stark disagrees. Henry then asks Tony why he's come, as he's made the church where the AA meeting was held a target, and Tony apologizes. Tony then explains that there's an Iron Man suit on the roof of the church which he'll use to flee. He then says that H.A.M.M.E.R will come busting in the moment he activates the armor, and tells Henry to tell nothing but the truth when he gets interrogated.
A flashback is then shown, revealing that Stark had set up a contingency plan in the event that the Stark Industries mail server was ever compromised. The system was set up with Henry, Maria, Pepper, and James Rhodes, and is basically an e-mail panic room. By typing in a specific code into the address bar and sending it, the e-mail will bounce back as an un-sendable and stay in the inbox, preventing anyone from tracking them. But the code is actually used to ping, and any of the five people who check the e-mail can see that someone is trying to contact someone else.
Back in the present, Henry meets James Rhodes after pinging him with the e-mail panic room. Henry pleads with Jim to get Tony to turn himself in, and War Machine agrees to. He manages to sneak up on Tony (as Tony is still using the Renaissance Armor with its outdated tech) and tries to convince Iron Man to turn himself in. Tony refuses, and then tells Jim that they have to 'battle' to ensure that Osborn doesn't think that War Machine is colluding with Tony. The two have an aerial engagement where Tony manages to blast out War Machine's weapons.
At Austin, Maria Hill breaks into Futurepharm, only to find that the Controller is there, plugged into a machine that's connected to people that she saw in missing people posters outside. He has been kidnapping them, evidently.
Meanwhile, Tony and Jim are still fighting, and Tony fires off a shot that breaches the War Machine armor. His plan is then revealed - Tony breached the War Machine on purpose because he didn't want Jim following him when he made his escape to his next armory - which was underwater. But the repulsor output from their fight catches H.A.M.M.E.R.'s attention, and when Osborn learns that Tony is fleeing to the seas, he opens up a line to Namor and tasks him with killing Stark.
Part Five: The High-End Technology of Ultramodern Destruction
At the Cascade Mountains in Washington, Pepper saves a music school that's crumbling due to an earthquake. We learn that her armor was built for heavy rescue and recovery, and that it has no armaments except for defensive and protective equipment. At an undisclosed H.A.M.M.E.R. base, Osborn is tracking the suit and is trying to learn what its capabilities are. He orders a commercial flight to be shot down to test her. Pepper uses her force-fields to successfully catch the plane, but upon landing it, becomes arrested by H.A.M.M.E.R personnel.
In the Red Sea, Tony is at a deep sea laboratory where he's working on his deep-sea Iron Man suit while connected to a repulsor terminal that continues deleting his mind. As he puts on his armor, he is suddenly attacked by Namor. Tony easily disables his three Atlantean guards, and starts fighting Namor. Tony smartly fires at a sewage pipe in the deep sea laboratory, enabling him to weaken Namor enough to suffocate him. He then flees.
At Futurepharm, Austin, Maria Hill tries to disable the Controller. The Controller senses her and activates the kidnapped mind-controlled people. Maria doesn't want to injure the mind-controlled, and they capture her and bring her to the Controller. The Controller puts a disc behind her neck and takes total command of her.
The issue ends with Osborn meeting with the Hood and Madame Masque, and tells them that a bounty is set up. A billion euros in gold and the thanks of a grateful nation for any villain that can kill Tony Stark.
Part Six: Some King of the World
H.A.M.M.E.R. personnel recover the helmet from Tony Stark's deep-sea suit at a beach. In Bayeux, France, Tony is at a tech fair, trying to find consumer-grade technology to downgrade his Iron Man suit. But his cover gets blown by some geek who probably wants to trade him for a piece of tech that consumers can't buy, and he is forced to flee. At Futurepharm, Maria manages to break free from the Controller.
In Avengers Tower, Pepper Potts is chained up as Norman Osborn interrogates her. She tells him that her suit is only built for rescue and recovery, and when Osborn wants to analyze the suit, she tells him that she doesn't know how to remove the armor. Osborn then asks her where Stark is, and Pepper replies that she doesn't know. Back in Bayeux, Shockwave comes after Tony, but he easily defeats him. In Futurepharm, Maria destroys the Controller's machines, setting the people free.
At Avengers Tower, Pepper states that all of her equipment and her role as superheroine is all legal and registered from the time in the Order. Osborn then gives her a proposition: that she allow him to look at the repulsor tech in her chest to power the Iron Man suits that Osborn managed to seize. Pepper refuses, and Osborn then tells her that if she uses her suit again, she'll be arrested or shot down. Back at Futurepharm, Maria manages to get the hard drive.
Madame Masque meets with Osborn at Avengers Tower, and he shows her a database that Stark left behind - revealing all the armories that are still up and running. He states that the Hood's soldiers are 'scrubs' and that H.A.M.M.E.R.'s jurisdiction is limited to the United States, so he tells her that she's in charge of killing Stark.
The issue ends with Pepper ignoring Osborn's threats and going after Tony.
Part Seven: The Shape of the World These Days
Tony is in Arkkangelsk, Russia, flying in his Classic Red & Gold armor when he gets shot down by surface-to-air missiles. He suddenly comes face to face with Crimson Dynamo (Dmitri Bukharin), who nearly kills him before recognizing that Tony is wearing an old armor. At Newark, New Jersey, Maria Hill has gone into hiding there.
In the Holland Tunnel, inside an ambulance, Pepper is checked out by the doctor that put the repulsor technology in her chest. He tells her that her repulsor is working fine, and coins the name 'Rescue' for her new suit. Pepper leaves immediately when J.A.R.V.I.S. reports interesting repulsor activity in Russia as well as a grain silo explosion in Berkley, Massachusetts.
Back in Russia, Dmitri and Tony are talking as Tony explains his situation. Dmitri suggests that Tony throws himself into a volcano, vaporizing his entire brain in an instant, but Tony replies that it's not that bad yet. His Iron Man armor has been wrecked during the fight with Dmitri, and so he borrows the Crimson Dynamo armor to get to his next armory - in Kirensk. In Massachusetts, Rescue manages to save personnel from the grain silo explosion, and heads for Russia. Osborn, tracking Rescue, contacts Dmitri to grant H.A.M.M.E.R. permission to enter Russia, but Dmitri refuses. Osborn gets angry and hurls his computer again.
In New York, Maria Hill finds Black Widow. Back in Russia, Tony (in the Crimson Dynamo) nearly kills Pepper because he doesn't recognize the Rescue armor. As they fight, Madame Masque is watching them through the scope of a sniper rifle, and has her crosshairs on Pepper.
Part Eight: The Danger We're All In
Tony finally recognizes Pepper, and when they kiss, Madame Masque chooses not to shoot them. Back in New York, Maria Hill tries to get Black Widow to hand the hard drive over to Captain America, but Natasha refuses to compromise Bucky and states that rumor says that Maria might have snapped. She leaves on the rooftops, but Maria chases after her. In Russia, Pepper and Tony have made it to the Kirensk armory, where Tony explains how bad his condition is deteriorating. Madame Masque is seen approaching the armory.
As Maria Hill chases after Natasha, H.A.M.M.E.R. agents using repulsor technology swoop in to get them. When the agents manage to corner Maria, Maria pleads with Natasha to shoot the hard drive, rather than to let it fall into enemy hands. Natasha is finally convinced that it must be important, and saves Maria from the agents.
Back in Russia, while Tony is out cutting firewood, Madame Masque sneaks in and holds Pepper hostage. Tony returns to the armory and is shocked to find that Masque has Pepper's repulsor hooked up to a car battery and is torturing her with it. Tony then drops onto his knees and begs Masque to stops. She then goes into a disturbing monologue and sits on top of the supine Tony, taking off her mask and shows Tony her scarred face.
Part Nine: Titan of the Nuclear Age
Tony and Masque have an extended conversation about their past love affair together, while Pepper manages to activate control of her armor. In New York, Black Widow and Maria Hill have a fight about the psychological scars that the Controller's mind-control left on Maria. Natasha then tells her that they'll rendezvous with Bucky to give him the hard drive, but that she needs to pull it together.
In Russia, Madame Masque puts her golden mask onto Tony's face, and sees in the mask's reflection that Pepper is remotely activating Rescue. She tries to shoot Pepper, but Tony trips her and Rescue manages to stop the bullets. Rescue then frees Pepper. Masque then asks Tony if he'll choose her or Pepper, and when Tony chooses Pepper, she shoots an oil drum, causing a massive explosion. Back in New York, Maria Hill has a flashback to the Controller and has to be put to sleep by Natasha. Natasha then checks the hard drive and meets a specialist who tells her that the drive is Stark proprietary tech.
The explosion at the Kirensk armory doesn't kill anyone, and the Rescue armor manages to seize hold of Masque. Pepper then tells Tony to run, and when Rescue's solar reserves run out, Pepper and Masque engage in a one-on-one fistfight. Tony flees to Afghanistan.
Part Ten: Ashes & Snow
At Kirensk, Madame Masque contacts Osborn, telling him that Pepper is dead and that she's attained the Rescue armor. In Almaty, Kazakhstan, Tony hitchhikes on a truck to a town with internet, and sends an e-mail to Maria using the panic room - since he's forgotten that you're not supposed to use it. He then suits up and continues to Afghanistan, heading for Starklab Double Zero. In the Helicarrier, Osborn is in contact with Dmitri again, and blackmails him into letting H.A.M.M.E.R. enter Russian airspace by telling Dmitri that he has intel on a Chechnyan splinter cell that's manufacturing an A-bomb. Dmitri concedes, but feels remorseful for selling out Tony.
At Kirensk, Madame Masque (and the Rescue armor) are picked up by the Helicarrier. The e-mail that Tony sent to Maria Hill is picked up by Walsh, who brings it to Hand. Walsh also feels remorseful that he ratted Tony out. In Afghanistan, Tony has fallen asleep in his armor, and he gets shot down by insurgents with a RPG. He crash-lands and evacuates the armor.
Back in New York, Black Widow and Maria Hill are ambushed by H.A.M.M.E.R. personnel while trying to rendezvous with Bucky, and brought into custody. Captain America watches from afar, but does not intervene. In the Helicarrier, Osborn debriefs Madame Masque and is about to strangle her when Victoria Hand enters, telling him that they caught Maria Hill.
Part Eleven: Kids with Guns v.s. The Eternal Angel of Death
In Afghanistan, Stark enters the Starklab Double Zero. He manages to start up the Iron Man Mark I, but before he can finish the process, he is shot in the neck by two child insurgents. At Avengers Tower, Maria Hill and Black Widow are held in cells, and Walsh manages to locate the repulsor signature of Stark. When he brings the information to Osborn, Osborn is gleeful and confides in Walsh about his plans to kill Stark. Osborn suits up as the Iron Patriot.
Back in Afghanistan, Tony is still alive and asks the kids what they want. The children reply that he's the great warlord, the 'eternal angel of death,' and asks him to make them great men of war. Tony Stark refuses, and tells them to either kill him or get out. The children freeze up, and Tony kicks them out. He then starts up the Mark I and begins fleeing to Dubai.
In the Helicarrier, Victoria Hand finds that Madame Masque is inside the Crimson Dynamo armor that was recovered from Kirensk. Masque reveals that Pepper has been posing as her, and that she was locked inside the armor. Pepper then goes the free Maria Hill and Natasha, and J.A.R.V.I.S. activates the Rescue armor, uploading a virus into the H.A.M.M.E.R. mainframe that disables all of the Iron Man armors that Osborn got ahold of.
Walsh, in his guilt, tries to trick Osborn and tells him (via intercom) that Tony is heading east - to Pakistan. The Iron Patriot goes after Iron Man.
Part Twelve: World's Most Wanted, Conclusion
In Avengers Tower, Victoria Hand is trying to find Pepper. Iron Patriot is unable to locate Stark (as Walsh is feeding him bad intel on purpose), and he loses his temper. Gormley, Walsh's supervisor, learns about what Walsh is doing, and has him arrested. Gormley then takes over the intercom, and redirects Iron Patriot back to where Iron Man is.
Back in Avengers Tower, Pepper disables H.A.M.M.E.R. guards with the repulsor in her chest, and she, Maria, and Natasha make their way up to the 33rd floor to RV with Rescue, as well as retrieve the hard drive. Maria and Hill manage to get the drive. In Dubai, Iron Patriot finally locates Tony, and the two begin fighting. Tony's mind is nearly gone by now, and he's struggling to hold his own against Osborn.
Pepper, meanwhile, has managed to find Rescue and suits up. J.A.R.V.I.S. then informs Pepper that its informed the world's media outlets that Osborn is in Dubai, attempting to murder Tony Stark. The world's media flocks to Dubai while Maria and Natasha manage to escape Avengers Tower. As Iron Patriot is about to kill Tony, Victoria Hand suddenly tells him to stop, as the cameras are on him. Iron Patriot concedes, and Tony Stark's last words are: "I win."
On the Helicarrier, the doctor explains to Osborn that Stark's consciousness is now-gone. His can still respond to stimuli, but his whole brain is damaged - even the part of him that knows how to breathe. Osborn then tells the doctor to pull the plug on Tony, but the doctor tells him that legally they can't, as the Helicarrier is a flying embassy. The doctor explains that Tony has a will, and that his power of attorney was given to his personal physician. Only Tony Stark's doctor can make the end-of-life decision.
In a motel in Broxton, Oklaholma, Doctor Donald Blake receives a call about Tony Stark. He is in the motel with Pepper, Maria, Natasha, and Bucky.