When Davos, the dying leader of the reclusive Vedeenan people, prophesies that Sheppard's team will soon be caught in a Wraith ambush, even the skeptical McKay and Sheppard have to admit that precautions appear to be in order.
Keller brings Davos to Atlantis for medical treatment while the team, forewarned by the venerable man, turns the tables on their attackers. They ambush the ambush with a pair of Puddle Jumpers. The Wraith leader they capture is the same Wraith with whom Sheppard once cooperated to escape a Genii prison. He claims that he only tried to ambush the team in order to talk to them.
The team locks up the Wraith in Atlantis and hears him out. It turns out that he has news of dire importance: In the ongoing war between the Replicators and the Wraith, the Replicators have begun exterminating entire human civilizations to wipe out the Wraith's food source. Tens of thousands of people have already died in this genocide. This Wraith wants to collaborate with McKay to reprogram the Replicators to end the war.
As Carter contemplates whether or not to trust the Wraith, Davos telepathically shows her a vision of a devastating Replicator attack on Atlantis. Later, he shows Teyla a vision of Sheppard preparing to fire drone weapons against a Wraith ship. Davos swears that he has never been wrong, and Dr. Keller confirms that his visions are the real deal: he possesses genetic advancements like those of highly evolved Ancients. Unfortunately, Davos can't tell Carter what actions of hers will or will not lead to the terrible consequences he foresees.
The stakes get even higher when the Wraith's hive ship, which has been secretly tracking its master's movements, arrives in orbit above the planet. His people now know Atlantis's location, although he promises they won't publicize it unless Atlantis fires on them.
Carter decides to let McKay and the Wraith begin the reprogramming project, but soon a second hive ship zeroes in on the city. The Wraith insists that he's not responsible, and McKay speculates that this second ship is merely curious to know what a lone hive is doing at such a remote planet. If that's true, they can just cloak the city and hide from the second ship until the first persuades it to leave.
If the two ships are planning to betray and attack Atlantis, however, the city will be unshielded and vulnerable as long as the cloak is active. Carter must decide whether to trust Sheppard's Wraith and cloak the city, or take the safer path and raise shields. The future of Atlantis depends on her making the right call.