Dana Mercer lives a relatively quiet life as a journalism student in Manhattan, but that all changes when her brother, Alex, shows up on her doorstep. Though they haven't spoken in years, he shares with her the top secret research he's been performing for Gentek, and though he leaves to continue the project, he promises to continue sending her information. Using the evidence she receives in the mail, Dana begins investigating the goals of the Gentek corporation, also discovering disturbing connections to the U.S. government.
Her investigation is halted when Blackwatch invades her apartment, but before they can interrogate her, Alex infiltrates the apartment and kills the soldiers. They evade the remaining guards and retreat to a safehouse Dana has prepared. She's surprised to find that her brother has dramatically changed: he's America's number one terrorist, he has mysterious, inhuman abilities, and he has a painful case of amnesia. Continuing their work together, Dana provides Alex with leads in the hopes he may discover the origin of his powers and bring down Gentek.
Their collaboration ends when a leader hunter smashes through the wall of the safehouse and kidnaps Dana, taking her to Elizabethe Greene. Alex hunts down Greene and demands Dana back, but Greene replies that Dana is now "one of us" and attacks Alex. Alex wins the fight and searches the area, finding his sister unconscious. He drops her off at Dr. Ragland's work, leaving to continue his mission before she awakens.
In the sequel, Dana contacts Heller and tells him his daughter Amaya is still alive. Trying to locate Amaya, she tells Heller to hold off Mercer and Blackwatch. She stays in contact with Heller over phone and provides him with advice and additional commentary over the course of the events.
After Heller consumes Mercer, the player gets to see Alex' memories of a conversation he had with Dana. She tells Mercer that she once had a brother who played with her and cared for her, but that as far as she knows, that brother is dead. Alex then explains to her that he is now beyond life and death.
At the end, Dana and Amaya reunite with Heller.