As soon as it's airborne, Trent and the cloaked Skedar make their move, but Joanna is there to stop them. She poses as a member of the President's entourage to gain access to the air base where Air Force One is stationed, and successfully conceals herself aboard the plane. Having aided the remnants of the Maian delegation, Joanna can return to the matter of the President and dataDyne's designs against him. He was a bodyguard for the Ambassador who had been flying in at the head of the specialist team. The particular Maian she manages to rescue goes by the name of Elvis. Upon breaking into the medlab, Joanna finally discovers the Institute's secret - their allies are Maians, the alien race commonly known as Greys.

Briefed to rescue any survivors and retrieve their equipment, Joanna is dropped in to link up with another Carrington Institute agent. The Maian specialists have been intercepted and brought down by the conspirators, with survivors and wreckage alike being transported to Area 51 in Nevada. Once Trent discloses the plan to usurp the Presidential position, Jo radios the news back to base, only to find another, more urgent task requires her attention before further action can be taken against Trent. It is here that she learns of the involvement of Trent Easton, head of the NSA, and of the strange Nordic men that appear to be in control of the whole deadly scheme. Joanna is dispatched to Chicago to spy on a conspirators' meeting at the G5 Building, a front for the dataDyne Corp. However, Carrington has heard enough to take the drastic step of summoning a team of Maian specialists to Earth. Joanna rescues the head of the Institute, but is unable to prevent dataDyne from taking back Dr. Unknown to them, the AI is already at the villa, where it was being questioned by Carrington on dataDyne's future plans. They demand the return of the AI-their 'property'-in exchange for his life. In response to this incursion dataDyne makes Daniel Carrington a personal target and takes him hostage two days later at his private villa. When the alarm is raised, Joanna has to fight her way up the tower to reach the helipad, which presents her only means of escape via dropship. Caroll' is an AI created by dataDyne itself but she continues with her task of escorting the doctor to safety. Upon rendezvous, she is surprised to discover that this 'Dr. Untried agent Joanna Dark is assigned a mission involving the extraction of a scientist from the high security research area beneath the dataDyne skyscraper.

There are also four bonus missions known as Special Assignments that are unlocked once the player has completed the respective difficulties of the campaign.

The campaign is divided into nine missions comprised of 1 to 3 levels each.

11.1 Rare Replay and Xbox One Backwards Compatibility.

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