After being fired from Stark Industries for refusing to stop working on the questionable and dangerous Project P.R.O.T.E.A.N., Kearson DeWitt sought revenge on Tony Stark. He began working with A.I.M. and revived Project P.R.O.T.E.A.N., evolving it into Project Ultimo. Using P.R.O.T.E.A.N., DeWitt was able to merge himself physically and mentally with the A.I. Ultimo and upgrade his men with P.R.O.T.E.A.N. implants.
On DeWitt's command, the S.H.I.E.L.D Helicarrier was attacked by A.I.M. forces. As several A.I.M. Gunships opened fire on the Helicarrier, S.H.I.E.L.D. director Nick Fury alerted his troops and ordered them to prepare for battle. One of the P.R.O.T.E.A.N. Hybrids broke into the Helicarrier's command center and grabbed Pepper Potts, throwing her off the Helicarrier. Tony Stark quickly donned the Mark VI armor, flew after her and grabbed her before she reached the ocean. Due to the armor's limited capabilities, he was unable to fly her back up, and had to jump across several gunships before placing her in the care of a S.H.I.E.L.D. pilot.
Stark fought against P.R.O.T.E.A.N. Hybrids and A.I.M. Drones while protecting the Helicarrier's repulsor engines and his own personal plane. He then boarded the plane and had James Rhodes fly it away from the Helicarrier to drive the A.I.M. forces away from it.
A.I.M. then deployed an Arc Armiger onto the Helicarrier. Fury requested assistance. Knowing that it was a trap to lure Stark out, Rhodes insisted that he stay on the plane while he donned the War Machine armor and defeated the Armiger.
Once the Armiger was defeated, Tony Stark informed the others that it could not be killed due to the fact that it had been enhanced by P.R.O.T.E.A.N. and could heal and rebuild itself. Instead, he planned to reprogram it and use it to his own ends. This was a success, and the Armiger proved essential to stopping DeWitt/Ultimo from unleashing Project Greengrid from an A.I.M. base in Malaysia.
- In the PSP and Wii versions of the game, A.I.M.'s forces are led by a mercenary known as Mauler, who plants several bombs on the Helicarrier in an attempt to bring it down. Iron Man must disarm the bombs and defeat Mauler. After his defeat, Mauler informs Iron Man of the incoming Arc Armiger and offers to help him defeat it.