Project Noah takes place in Colorado. The government is testing a super-soldier program on a dozen death row inmates in addition to patient zero, Tim Fanning. While the test subjects adapt to the injections, they become unpredictably violent. The faculty cannot control them. Dr. Lear, the one who synthesizes the serum, believes that a child may adapt without the violent tendencies to which the adults are subject, so he tasks Brad Wolgast, an FBI agent, wiht tracking down a specific girl.
Amy Bellafonte is a six-year-old. She lives at a convent because she's an orphan. In order to obtain permission to escort her to Dr. Lear's lab, Wolgast also takes along one of the nuns, Sister Lacey. Both Lacey and Amy are exposed to the serum, Lacey accidentally, but it takes immediate effect on Amy. According to Dr. Lear's hypothesis, Amy experiences no negative side-effects.
During this testing, the twelve inmates escape after one of them, Babcokc, develops psychic powers. They essentially destroy the research facility and everyone in it, but Amy and Wolgast survive. They hide away in a safe house, watching the news as the contagion spreads. Eventually Wolgast, a regular human, dies of radiation exposure.
90 years later, Amy has survived the contagion, having only aged to look like a teenager thanks to the strength of the serum. She checks in to a survivor colony, but the situation is desperate. Babcock is in the area, interfering with people's brains. When Amy arrives, she is told that they have been receiving occasional radio messages from a presumed larger colony in Colorado. She arranges a crew to try and trace the signal manually.
In Vegas the party comes across the Haven, a refuge space. At least that's what they assume. Contrary to initial conclusions, it is actually Babcock's headquarters. After serious negotiations, he allows the people to leave. He does demand, in return, that they bring him human blood. The virus has essentially turned people into vampires, called "virals." Amy, having lived this scenario for decades now, devises a plan to defeat Babcock, theorizing that his death will lead to the immediate deaths of all of the virals. She lures him into the basement where Sister Lacey detonates an explosive device.
Both Lacey and Babcock die, followed by the consequent deaths of the virals. The surviving members of the scouting party travel to Roswell where they find a mysterious document dated from the future. It describes The Roswell Massacre. Nobody knows what it means.
