During a rainy night at the Stark Tower Pepper Potts and Happy Hogan enter a dimly-lit room, approaching with caution the dark silhouette of a bulky suit of metal, the original Iron Man Armor, sitting on the floor leaning against the wall. In her inner monologue, Pepper introduces herself as a 31-year-old top scientist at the company who is secretly in love with her boss, and admits to herself that it sounds cliché. As she reaches out to the suit's helmet, she recalls that she lets him call her "Pepper," one of the many things she lets him get away with. Under the suit's mask, two eyes suddenly open up, startling Pepper. Brushing aside her opening remarks, Pepper reveals that this is the story of how she died. Recognizing Tony Stark inside the suit, Pepper screams for him to help her get the armor off their boss.
Pepper and Happy have disassembled most of the armor, uncovering a bruised and scratched Tony underneath. When they reach the helmet, Tony stops them so they don't take off the chest plate since its electromagnets are keeping shrapnel near his heart from getting closer. He explains he just needed to charge it, and unplugs the chest plate from a cable that was connecting it to the wall. Tony turns his attention to his computers, brushing aside Pepper's worry while sardonically going over the multiple injuries he's suffered. He declares that his suit is not enough as it is, and asserts that he can make it better, and more than a weapon. When Happy suggests getting a doctor, Tony remarks that he doesn't believe in qualifications, and cites having hired a boxer like Happy as a chauffeur. Stating that he made the armor out of garbage in a cave, Tony challenges them to see what he's capable of when really trying. Tony sits at his computer and dismisses his two employees and jokes that they're fired until Monday. Pepper is perplexed that the man she had spent weeks thinking was dead is now asking for space to focus and create.
The following day, Pepper is sleeping at a desk. Her inner monologue explains neither she or Happy obeyed and are keeping Tony company alongside his butler Jarvis, to the point that Pepper hasn't left the penthouse to help Stark. She has been studying so much about different technologies she passed out reading. The shadow of Tony's armor falls on the room as Tony's voice wakes her up. Pepper recalls in her monologue dreaming of clawing at a parasite attached to her chest until her nails peeled off. As she's rousing herself, Pepper notices that Tony got back into the armor. He explains that he's testing the suit's new on-board dermal regenerators. Tony takes off the helmet and presents his pristine face, to Pepper's admiration. She touches Tony's face, admiring the suit's work. Tony hypothesizes the suit could work like a mobile hospital. Pepper deduces that it takes more than dermal regenerators, and Stark explains the suit is run by semi-autonomous computational machinery which coordinates with his brain waves. Tony elaborates that the armor can also probe inside himself, repairing organs and bones with its technology. He continues, disclosing that while in captivity, he discovered he's better at figuring out ways to stay alive, so the suit's new and sole purpose is to keep him secure and alive. Extending his left arm, Tony explains that before putting the glove on, it had three fractures. He invites Pepper to remove the gauntlet and see how it is repaired. Pepper slides it off, but Tony's arm is skinless underneath. Tony goes into shock as Happy and Jarvis rush to help put the glove on, and Tony is instantly relieved when they succeed, quipping about there being a few bugs to work out. Jarvis and Happy help Tony to his computer as he explains that the suit must have replaced his skin with itself because it calculated that, logically, iron skin would offer more protection. Tony asks his friends to help him take off the rest of the suit since the arm is the only part where the armor got that far. As they do so, he explains he just needs to rebuild the suit's supervisory algorithm to make it regenerate the skin it took. Pepper points out she refreshed herself on the company's latest A.I. and biomedical research, and Tony commends her. Placing his hand on Pepper's shoulder, Tony orders Jarvis and Happy to get the manufacturing plants on standby while he and Pepper solve the armor's issue.
As Pepper and Tony are shown working together over an extended period of time, in her monologue she relishes that he treats her like an equal. Pepper expresses she has noticed Tony unconsciously taps his foot when he's really focused, something that he hates, but she loves it and she loves him. Eventually, Tony opens up to Pepper, admitting that he doesn't think he likes himself anymore because he was faced with the prospect of dying as an arms manufacturer who was seen as a profiteer of death, and thought it wasn't fair since he had never killed anyone and only made the tools. Tony begins to tear up as he recalls then making the armor and killing every one of his captors. Pepper approaches Tony as he elaborates that he wants to be remembered as a hero who helped people, and that his suit is his first step to redemption since he can help people with it. As he turns to Pepper and caresses her face, Tony expresses that he also didn't want to postpone the people who love him, and he and Pepper share a kiss. Tony slides his arm down Pepper's back, and she tells him that they will have time to get intimate once they get the armor off him. Time passes, and Tony and Pepper have split up their working force, and they're running experiments away from each other. Sunday comes and Jarvis approaches Pepper with breakfast. She notices that he addresses her "ma'am" for the first time, and wonders if he's aware her and Tony's development. Stark enters the room, shocking both of them. He is fully clad in the armor, with limbs slightly crooked and his head tilted. A white fluid is leaking off the suit's crevices. He obliviously asks Pepper what is wrong.
Pepper asks Tony why did he put the suit back on, prompting Tony to only just now realize he did. Pepper rushes to a computer and informs Tony that his entire skin has been dissolved by the armor. She warns Tony against taking it off since it would kill him at this point, but she's left speechless when Tony asks why would he ever want to do that. After dismissing it as a joke, Tony sits at his computer. He assures Pepper and Jarvis that it's still him inside the suit and he will fix this issue. He asks her and Jarvis to pull together a nutritional isosolution at the lab downstairs. When they return some minutes later, they find Tony on the floor. At his command, the building initiates an isolation protocol, and a giant glass panel slides from above, shutting Pepper and Jarvis out. Tony feebly tells her that he feels different and needs a moment to collect himself. Pepper tells him she's going to use the laboratory scanners to look inside the suit. To her uneasiness, the screens show Tony's entire body is breaking down; wires from the suit are deep inside his brain, his skull is gone, and he'll never be able to leave the suit again, since most of his insides are undifferentiated meat. When she tells him this with tears in her eyes, Tony calmly raises his head. With his eyeballs almost protruding from the faceplate's slits, Tony expresses that it sounds fine to him. Getting up, Tony tells her that an iron skull is better, and he limps away despite her pleas. The white substance has battered Tony's armor, with exposed wires hanging from its crevices. He turns around, apologizes to Pepper to standing her up and leaves to do work. In her inner monologue, Pepper explains that Tony has kicked the building into lockdown, leaving his friends trapped and unable to do anything but wait. She notices that Tony is focused building something and he isn't tapping his foot anymore.
Sometime later, after Happy has joined Pepper and Jarvis, the glass panel slides open as Tony expresses through the intercom that he has had an epiphany. Jarvis and Happy enter the laboratory with caution. Pepper tries to reason with Tony, but he cuts her off, explaining how the human body is flawed but he can do better and protect everyone. The glass panel slams downward, separating Pepper from Jarvis and Happy. The fire suppression system is turned on, sucking all the oxygen from the room and knocking Jarvis and Happy. Tony's hands pull them away from behind. Pepper returns to Tony's penthouse to observe the laboratory's camera feeds, all of which except one are offline. Tony forces both Jarvis and Happy into a copy of his armor, mutilating their bodies in the process. After some time, the suit gets up and shambles out of view to help Tony. The building's lockdown is suddenly lifted, and Pepper worries of what Tony could have done all night without interference and with the help of one of the most advanced automated manufacturing facilities in the world. Pepper looks outside a window and is appalled to see a crowd outside the building gathering around another copy of the armor. A recorded voice entices people to climb inside to fix their illnesses. An office chair plummets between the armor and the excited crowd, and from the broken window above, Pepper desperately warns them against getting in the suit. Pepper steps back, noticing her effort had the opposite effect, and people are now fighting to climb in faster. She breaks down as her hopes that it's only one suit outside are quenched when she hears many screams across the city, all silenced as soon as the suits do their work. Pepper realizes the same will happen to her as Tony appears behind her, resting his hand upon her shoulder. Piles of flesh are oozing out the battered armor as Tony calls Pepper's nickname while leading her to another copy of his armor hanging from the ceiling in his lab, one tailored for her female physique.
