A Wraith hive ship arrives in orbit above Atlantis. In the cloaked city below, everyone is stunned when Michael radios down with an unnerving request: He wants to negotiate an alliance.
Frustrated in their quest to locate Earth, the Wraith are now running short of their food - humans - and have begun fighting among themselves. For this reason, Michael seeks a weaponized version of Dr. Beckett's anti-Wraith retrovirus, which briefly gave him a human body. He wants to deploy it against rival hives, turning them human and feasting on the results. His hive will gain food and power, and the Atlantis team can deal a fatal blow to thousands of their enemies.
Weir and her senior staff decide that such a payoff is worth the immense risk of trusting the Wraith, and soon the new allies are working side-by-side. With the help of a Wraith scientist, Beckett and Zelenka struggle to weaponize the retrovirus, while McKay coordinates with the hive's crew to practice bypassing a hive ship's defenses.
The Wraith, however, make everyone uneasy. Worse, their first attempt to target another ship with the new weapon ends in disaster: Their enemies discover the canisters of the retrovirus too soon and open fire. Michael's hive ship and the Daedalus barely escape intact.
The imperious Queen of Michael's hive now threatens to reveal Atlantis's existence to all the Wraith if the humans won't design a reliable delivery system for the weapon. McKay, frustrated, demands that she help by allowing him free access to every last piece of information about Wraith ships. To his astonishment, she agrees, downloading a virtual encyclopedia of technical specs to Atlantis's computers.
Zelenka delves into this goldmine of strategic intelligence while McKay - escorted by Ronon - explores the hive itself and discovers a perfect delivery point for the retrovirus in the atmospheric system. With that, they're ready to attempt a second attack: The Daedalus will beam the canister onto another enemy hive. McKay and Ronon will observe from Michael's ship. Sheppard will observe from the Daedalus.
But soon after the mission is underway, Zelenka discovers that the electronic Wraith encyclopedia was infected with a virus of its own - and now that virus is loose in Atlantis's computers. It's too late to warn the Daedalus, which drops out of hyperspace to find itself trapped under a ferocious bombardment from two hives - the enemy vessel and Michael's ship. The alliance was nothing but a ruse; the real plans of the Wraith are far more sinister. Far from giving up on finding Earth, they've just tricked the Atlantis team into giving them exactly the information they need to get there.