When John Sheppard's father Patrick dies, Sheppard and Ronon visit Earth for the funeral. Sheppard's feelings are more complicated than simple grief. Over the years, his difficult relationship with his wealthy, domineering father weakened all his family ties. His older brother, Dave, greets him coolly, and when Sheppard's ex-wife, Nancy, who always liked Patrick, stops by the wake, she and Sheppard barely know what to say to each other.
Then a mysterious young woman named Ava Dixon accosts Sheppard and Ronon with news that forces them to leave the wake immediately. Ava knows all about a recent top-secret incident in which Sheppard's team shut down Devlin Medical Technologies, a corporation doing dangerous research with nanites derived from Replicators. She claims that her boss, Dr. Richard Poole, who studied nanites for a division of Devlin, has secretly built an illegal, human-form Replicator. Three weeks ago, the Replicator escaped from Poole's lab, killing two guards. Though Poole has been trying to track it down privately, Ava has decided that she must come forward and seek help before more lives are lost.
Sheppard and Ronon arrest Poole and persuade him to accompany them and a team of Marines to a waterfront industrial park, where scans indicate that the Replicator is hiding.
Poole escapes from the group and confronts the Replicator on his own, convinced that he can talk it into surrendering. The Replicator kills him, and a massive chase ensues. The hunt ends when the Replicator, who has been shot, leaps off a crane into the water and vanishes. Divers can't find its body, and it no longer appears on any scanners. It has escaped.
With help from the SGC's Dr. Bill Lee and, surprisingly, from Nancy (who works for the Department of Homeland Security), Sheppard and Ronon search government records and Poole's encrypted files for clues that will help them find the Replicator. Dr. Lee makes a breakthrough when he discovers that the real Ava Dixon, whom Poole cared for deeply, died more than a year earlier. The Ava they've met is a Replicator programmed with the necessary social skills, ethics and emotions to be her replacement. Sheppard and Ronon hurry to confront her, but she has run away. Now two Replicators are on the loose.
Nancy gives Sheppard information about a warehouse that stores neutronium, an element that the injured Replicator will need to heal himself. Sheppard and Ronon plan a risky trap at the storage site and settle in to wait for the Replicator to take the bait. But even if it does, Ava's still missing. And Sheppard still has to answer to his brother for his abrupt departure from the wake. As Ronon points out with his trademark gift for understatement, Sheppard's having one hell of a week.