National Security Threats
Phil Coulson arranged a meeting with Obadiah Stane right after the Kidnapping of Tony Stark, to assess which kind of threats to National Security could pose the information Stark knew. Coulson met Stane at Stark Industries Headquarters under orders of Nick Fury. During the meeting, Stane made it clear that Stark knew very little of Homeland Security topics, as he was very focused with technology development and trusted the uses of that technology to James Rhodes and Stane himself.
Return of Tony Stark
Tony Stark returned to Los Angeles upon escaping from his kidnapping in Afghanistan and asked his assistant Pepper Potts to call for a press conference at Stark Industries Headquarters, where he was greeted by his business partner Obadiah Stane. During the press conference, Phil Coulson asked Potts to arrange an appointment with Stark to discuss the circumstances of his escape.
Stark declared to the press that his company would no longer manufacture weapons after watching soldiers die with the weapons built to protect them with his own eyes. Stark went to Arc Reactor powering the Headquarters, and tried to propose this technology as a new field of investigation to Stane, realizing that he already knew about the Miniaturized arc reactor in his chest.
Obadiah Stane recovered the armor prototype used by Stark to escape from the Ten Rings, and moved it to Los Angeles, closing Sector-16 of Stark Industries Headquarters in order to reverse-engineer his own version.
Stark sent Pepper Potts to find the shipping records of Stark Industries, so he can track down the illicit shipments and destroy them. While hacking into the system, she discovered that it was Obadiah Stane who hired the Ten Rings to kill Stark, and his plans for developing a new armor prototype.
Terrified for her discovery, Potts ran into Coulson and asked for S.H.I.E.L.D.'s assistance in stopping Stane, who tried to accelerate his plans of activating his armor. Stane found that his team of scientists could not create a miniature Arc Reactor to power the new suit, so he resolved to steal Stark's own reactor.
Potts accompanied Coulson and a team of agents to arrest Stane, but he easily defeated the agents using his new armor. Stane pursued Potts until Stark arrived in his own armor to battle Stane. Although Stane's armor had superior strength and was more heavily weaponized than Stark's, Stark managed to resist and save various civilians endangered by Stane's attempts to kill him. Stark tried to fly away out of Stane's range, only to realize that the heavier armor had also flying capabilities. Stark then devised a quick plan, reaching the Atmospheric freezing level to make Stane's armor freeze and crash into the ground.
Running out of power and with Stane still trying to kill him, Stark instructed Pepper Potts to overload the full-sized Arc Reactor, creating a huge pillar of blue light over the sky of Los Angeles that electrocuted Stane inside his armor, and causing a huge explosion when falling over the reactor.
After the fight, James Rhodes tried to get Stark into an ambulance to be checked for internal injuries. Unbeknownst to them, the ambulance was a cover S.H.I.E.L.D. vehicle sent to by Coulson in order to analyze his fighting strategy against Stane. Coulson also explained S.H.I.E.L.D.'s interest in Stark and offered to train him and prepare an alibi for the events surrounding the battle.
Stark checked press headlines dubbing he alter ego as "Iron Man" while preparing a press conference to explain the alibi provided by Coulson, in which Iron Man is announced as one of Stark's personal bodyguards. However, Stark instead announced his actual identity is Iron Man.
Iron Man located two shipments of Stark Industries-produced weapons scheduled to be decommissioned, that had been illegally diverted from a destination where they would have been destroyed. Stark contacted Pepper Potts at Stark Industries Headquarters tasking her and one of Stark's I.T. Department workers, Jesse to trace the IP address of the responsible of hacking the shipping routes. However, Jesse was deceived by an e-mail she thought came from his aunt, to let a malicious software sent by Cordo Gaines to invade Stark Industries mainframe.
Two days later, Jesse apologized to Stark and Potts, as it was her fault that Gaines obtained access to all information about Stark and his company. Potts discovered that there was Stark's outlays began to be redirected to front organizations with untraceable sources, forcing him to freeze all his assets until the crime is resolved, in order to calm his stockholders. Stark sent an advanced traceroute routine into the system from Stark Industries mainframe to track down the source system of the malicious code, locating it at Genoa, Italy.
A few hours later, Potts received a phone call from Stark, who informed her he managed to arrest the culprits, and invited her to come to Genoa, telling her that he was incarcerated for property damage so that she couldn't refuse to attend a party there.
Tony Stark's reveal of his identity as Iron Man brought an unexpected turn to the lives of the people close to him. For instance, Pepper Potts had to apologize in his behalf for his absence during a board meeting at Stark Industries Headquarters, as Stark was sent to Afghanistan to launch a Magna-Drone to clean several square miles of a Land mine-infested desert.
Pepper Potts, from the CEO office at Stark Industries Headquarters, phone called Tony Stark to check his business meeting with the representatives of Gorani Insurance in Germany, a company which backed most of his foreign factories.
Potts spoke to Stark, worried about his continuous delays. While on his way to the meeting, Stark found and captured a group of art thieves, calling Potts about one hour after his confrontation against the thieves to inform her of the situation. Potts lectured him about how these actions wouldn't help him to make to the meeting on time, without knowing that the capture of the thieves saved Gorani Insurance over one hundred million dollars.
During a mission to hijack an operation of the Ten Rings, Natasha Romanoff was assigned by Nick Fury to infiltrate Stark Industries under the guise of Natalie Rushman in order to get close to Tony Stark. For that purpose, she was interviewed by Bambi Arbogast and was hired as a notary public working in Stark Industries Headquarters. Romanoff spent some days undercover at Stark Industries, getting to know her environment and waiting for the opportunity to approach Tony Stark.
When Stark decided to claim Pepper Potts as his successor, Rushman overheard that Samantha Carlisle would be tasked with delivering the legal documents for the transfer of power to Tony Stark's Mansion in Malibu. Romanoff devised a plan to take Carlisle's place, using a trick learned from a contact retired from the KGB, poisoning her beverage to make her feel sick. Her plan worked, and she was tasked with the delivery, meeting Stark and, eventually, been assigned as his new assistant replacing Pepper Potts.
Stark Industries New CEO
Tony Stark drove to Los Angeles to meet Pepper Potts at Stark Industries Headquarters, trying to make amends with her for his behavior during his last birthday party, where he got drunk while donning the Iron Man Armor and confronted his friend James Rhodes. Bambi Arbogast, announced Stark's arrival to Pepper Potts who, at the moment, was dealing with the confiscation of the Mark II Armor by Lt. Colonel Rhodes. Potts was very mad at Stark for his behavior, and eluding the responsibilities he assumed when he revealed to the world that he was Iron Man.
Potts prompted Stark to abandon the office when Natasha Romanoff entered to confirm Potts' flight to New York City in order to attend the Stark Expo. Stark was amazed at how Romanoff maintained her cover as Natalie Rushman in Stark Industries. Left alone, Stark noticed the scale model of the Stark Expo, described by his father as his life's work, and realized that there was something hidden in the structure of the scale model.
Reunion with Aldrich Killian
Happy Hogan, now head of security at Stark Industries Headquarters, went to brief Pepper Potts about an idea he had to increase security in the building while reminding every employee that they have to wear their security badges. Hogan suggested to replace the entire janitorial staff with Tony Stark's unused Iron Man Armors, which were stored in the basement of his mansion wearing party hats, since he felt the human element of Human Resources was the biggest security point of vulnerability.
Potts congratulated Hogan for his new position as Head of Security but also revealed that the staff complaints rose 300 percent since he was appointed. Hogan took this as a compliment, as he considered it proof that there was something to hide. Bambi Arbogast announced that Potts' four o'clock appointment had arrived, and as Hogan tried to interfere, Potts dismissed Hogan in order to deal with her appointment, Aldrich Killian, a former co-worker who would make her feel uncomfortable with his advances.
However, she was then surprised to see the formerly-disabled Killian having improved his appearance and attitude. Hogan asked Killian about his security badge, but Potts told Hogan he could leave them alone. Hogan came across Eric Savin lounging in the waiting room and asked about his security badge, sensing something suspicious about him. Killian pitched to Potts one of his think tank's projects, Extremis, previously banned for being considered "immoral bio-tech research", for Stark Industries. Killian showed Potts a holographic image of the human brain, particularly his brain, and explained that the goal of Extremis was to harness humans' bioelectrical potential in order to upgrade their brain and entire DNA.
Meanwhile, Hogan received a call from Stark, who taunted him about his strictness as Head of Security, and Hogan replied that he quit being Iron Man's bodyguard due to the resulting humiliation. Hogan told Stark about Potts' reunion with Killian, and having run his credentials, remembered that they met Killian at a 1999 science conference in Switzerland. Hogan revealed the weirdness of Potts' reunion with Killian, as he was showing her his own brain, and advised Stark to pay more attention to her, as she the best thing to ever happen to him. Hogan announced he was going to follow Savin, as he looked very shifty, and revealed he missed how things were with Stark before he mixed up with the Avengers.
Killian continued explaining the potentials of Extremis to alter the DNA of any living organism. However, Potts also believed it could easiky create weapons such as enhanced soldiers or private armies, therefore declining to allow Stark Industries to join its development. Killian continued to insist that since Potts was the new CEO, she didn't have to listen to Stark but she refused despite her intrigue at Extremis. Potts then accompanied Killian to the exit, where he expressed his disappointment over the failed opportunity to cooperate, although he assured Potts that they would meet again, kissing her on the cheek. Hogan told Potts that her car was ready, and she returned to her office to retrieve her belongings. Meanwhile, Hogan took a photograph of the plates of Killian's car to investigate it.
Hiring Maria Hill
Maria Hill went to Los Angeles in order to join Stark Industries following the reveal of the HYDRA infiltration within S.H.I.E.L.D.. Hill was submitted to a series of polygraph tests at the Human Resources division.