A hive ship arrives in the Atlantis planet's star system and the team nervously tracks its approach for the planet. Rodney suggests they bring up the shields but Woolsey prefers to stay quiet and orders the cloak device engaged. The ship arrives in orbit but there's no attack. There is a file transmission but the file is corrupted. Rodney manages to decrypt part of it and it's a distress message from Todd the Wraith, saying that his crew needs Atlantis' help with some infection derived from Keller's anti-Wraith gene therapy.
Without enough data to make an informed decision and with no immediate threat, Woolsey authorizes Sheppard to take his team up in a cloaked jumper and make contact. There are no life signs but Rodney believes that the Wraith are in hibernation. They go on board and Rodney confirms that the Wraith are in their hibernation pods. However, there are neither a few Wraith conscious to wake the others, or any automatic wake-up signal. As Rodney accesses the original transmission from Todd, there's an unexplained power fluctuation. In the transmission, Todd explains that the Wraith crew are suffering from a plague caused by their treatment with Keller's gene therapy, and that they obtained it after hijacking the Daedalus
. The gene therapy cured the Wraith of their need to feed on living beings, but they began to get sick. Todd finishes the transmission by asking for helping, noting that if he and his crew die then there'll be no way to distribute the gene therapy among the other Wraith.
The team returns to Atlantis and Sheppard suggests they destroy the hive ship. However, Woolsey believes the IOA wants more information on the success of the gene therapy, which they're pushing as their solution to the Wraith problem. They consider not trying to find a cure and letting the Wraith die, but conclude that there's no guarantee every Wraith will catch the plague or die from it. They return to the hive ship with Lorne's team and Dr. Keller. The Marines spread out through the ship as Rodney tries to access the systems. One of the men, Williams, finds a melting wall. He contacts Sheppard and Lorne to inform them of his situation, but is interrupted when an unmasked Wraith soldier attacks him.
As Keller begins analyzing the plague, she's worried that she may be in over her head but Rodney assures her she'll do fine. Sheppard and the others look for Williams but find nothing but his gun. No life signs are showing up on their sensors, and Lorne and Sheppard find a dead-end corridor when the ship's schematics indicate no such thing. Rodney says that he downloaded the schematics from the ship's computer but something must be wrong. Teyla and Ronon find Williams' corpse and realize that he was partially eaten. Sheppard and Lorne finally lock on to a life sign and follow it to a hibernation chamber. A Wraith soldier ambushes Sheppard and he and Lorne manage to combine their gunfire and kill it. Examining the Wraith, they discover he was infected and lost his feeding hands. However, unable to obtain his normal sustenance, the Wraith soldier attacked Williams and tried to eat him.
Rodney has analyzed the system and informs everyone that the power fluctuations are getting worse, and that they are shutting down the Wraith hibernation pods. Sheppard orders a retreat but their route is cut off by another wall that wasn't there previously. They take the only other alternate route but find a vast pit penetrating the center of the hive ship.
The team returns to the bridge and Rodney concludes that the hive ship is somehow reconfiguring itself. Interference prevents them from contacting Atlantis for a rescue. Rodney warns that he can't keep ahead of the malfunctions and they only have one option: free Todd to get his aid. Releasing Todd will put him at risk since Keller hasn't found a cure, but they don't have any other choice. Fortunately, Todd isn't overcome with hunger and agrees to help them. He checks the ship and realizes that its organic structure has become infected with the disease. They can't land the ship in its current condition and Todd warns they only have four days before the ship reaches the point of no return. He goes to work with Keller to find a cure, while Rodney informs Sheppard that he has a way to stop the hibernation pods from opening. However, the procedure will suffocate the Wraith inside the pods. Sheppard orders Rodney to do it without telling Todd. However, he's unable to override one of the pods. Sheppard and others go there only to find that all of the pods are opened.
As the Marines hunt for the escaped Wraith, Todd finds a possible solution. He has Keller call in Sheppard, and then explains that there is a special healing process that involves an Eratos bug feeding on a Wraith, jump-starting his accelerated healing. It's potentially dangerous and the nearest planet with an Eratos bug is three days awhile. Sheppard refuses to endanger the ship by going there, and Todd accuses him of basing his decision on Wraith prejudice. Todd insists that they owe him and his crew for creating the gene therapy but Sheppard doesn't buy it and orders him into a cell.
The hive ship begins to collapse ahead of Todd's estimate, and a crack is spreading across the center of the ship. Sheppard orders the others to retreat to the forward section but Wraith soldiers ambush Ronon and another Marine. Teyla and the others get there and manage to save Ronon, but find their escape route blocked by another door. As the Wraith soldiers move in and the team is forced to open fire, Sheppard runs to the door and manages to get it open. They get out of the rear section just in time as Rodney seals the bulkheads and the ship splits in two. However, Rodney realizes that the change in the ship's mass has altered its trajectory, and it's falling out of orbit. Rodney tries to activate the thrusters but they need Todd's help. Sheppard tells their prisoner what the situation is but Todd would rather die once he learns the rest of his crew died when the back half broke off. Sheppard gives Todd his word that he'll get him to the Eratos bug if they survive the landing and Todd agrees to help.
On the bridge, Todd takes control of the hive ship's thrusters and tells Rodney to stop whining and get him as much power as he can. Rodney manages to get full power to the thrusters and Todd brings the nose of the ship up as it plummets toward the ocean below. He manages to level it off and they skip across the water to a relatively safe landing.
Later, Sheppard leaves the infirmary and meets with Woolsey, who informs him that everyone was evacuated safely and the ship half sunk just after they got everyone out. Sheppard insists on keeping his word and Woolsey notes the IOA won't like it. Sheppard points out that his honor aside, they need Todd to deploy the gene treatment. Woolsey agrees and Sheppard escorts Todd to the Stargate so he can travel to the planet with the Eratos bug. Todd is surprised that Sheppard kept his word and promises that he'll remember what happened.
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