Tony agreed to work on that problem, but also began tinkering with another idea—a suit of armor designed specifically for Potts. She only discovered the suit after Norman Osborn took over S.H.I.E.L.D., turned it into H.A.M.M.E.R., and tried to kill Stark after the events of SECRET INVASION. Osborn got especially mad when he accidentally launched a virus that Stark left in case the former Green Goblin attempted to illegally access the Super Hero Registration Database...which (of course) he did on his very first day.
When Stark planned to shut down his own mind to erase the last remaining copy of the Super Hero Registration database, he put Pepper in charge of shutting down his company as well. In a moment of frustration at the end of INVINCIBLE IRON MAN (2008) #10, she started trashing the office and discovered a secret lab with the very suit of armor designed just for her!
Dubbed the 1616 armor and kitted out with a J.A.R.V.I.S. artificial intelligence interface, the suit was specifically designed for emergency response operations, which led to her taking on the name Rescue. After saving a few people, Potts got captured by Osborn's H.A.M.M.E.R. agents—but got away because she and the armor parts were all registered.
From there, Pep tried to find the on-the-run Stark, eventually catching up with him in Russia. After a brief reunion, the duo was captured and tortured by the Super Villain called Madame Masque. Pepper managed to control the Rescue armor to free them both and give Iron Man time to escape.
In INVINCIBLE IRON MAN (2008) #17, Potts donned Masque's mask and took her place in Norman Osborn's operation, claiming to have killed Pepper and offering him the Rescue armor. She then used this as cover to free the captured Maria Hill and Black Widow. Meanwhile, Stark was defeated by Osborn just as his mind fully entered the deletion process, putting the hero in a vegetative state. Thanks to his will, Stark's body was passed along to the care of Dr. Donald Blake who was working with Hill, Widow, Potts, and Bucky Barnes (who was in the midst of his stint as Captain America) to figure out how to reboot Tony!