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The mystery of “Haunted” continues as Tony Stark, burdened by the ghosts of his past, journeys back to Omaha to get the answers he isn’t supposed to be searching for. Despite the warnings of Doc Samson and the opposition of corrupt government officials Norman Osborn and Jack Kooning, Tony has chosen to pursue the unexplainable actions of Gadget, and why it seems there is a connection between her death and those of several other seemingly disconnected people. Meanwhile, the manipulative and power-mad Mandarin is on the verge of unleashing the Extremis pandemic across the world, ready to cause the irreversible outbreak that will grant millions of people uncontrollable powers. All that stands in the way of Mandarin’s immeasurable chaos is Tony Stark, now armed in his classic iron suit and ready to battle both his demons and his greatest nemesis!
While trying to figure out what the missing people reports have in common, Stark is haunted by a vision of Sal, who reminds Stark of drug trial procedures. Sal vanishes just before Mrs. Rennies calls to tell Stark that his armor will be arriving soon. In Nebraska, Doc Samson convinces Captain Ultra to help track down the AWOL Stark.
Maya tells Mandarin that she's completed an airborne delivery system for Extremis, with a built-in programmed cell death (PCD) to swiftly kill the Extremis nanobots if they do not make contact with a host, to prevent them triggering a pandemic.
Meeting Dugan at a truckstop, Stark tells him the pattern of the Nebraska missing person cases match drug testing stages, suggesting they are being ecperimented on, and tells Dugan to check for DNA matches in the missing people.
At Gentechn the Mandarin is informed that Maya's PCD is impossible to crack. Moments later Kooning calls to tell Mandarin that Stark is still in Nebraska. As Stark picks up his model 04 armor at Council Bluffs airport, Dugan calls to say that all the missing persons share a common "junk" DNA sequence. Having only had time to don his helmet and one gauntlet, Stark is attacked by an Extremis-enhanced man, but Captain Ultra ans Samson arrive in time to help. Defeating the attacker, the three regroup at the Easy 8 Motel where Stark tells them about the missing perons. The "junk" DNA sequence they all share is a natural resistance to Extremis and the Mandarin is experimenting on them.