Infection

"Infection", originally named The Antidote, is the seventeenth episode of the fifth season of Stargate Atlantis.

Synopsis
After a Wraith Hive Ship shows up over Atlantis transmitting a distress call, the team discovers that its crew has been stricken with a disease they helped create.

Previously on Stargate Atlantis
Colonel Sheppard's team makes contact with Todd a board his hive ship in the hopes of stopping the Asurans. Todd hijacks the Daedalus in the hopes of destroying the Attero device by crashing the ship into M6H-987. However, Sheppard, with the help of a Traveler ship, creates a hyperspace window around the Daedalus, saving it moments before destruction. Meanwhile, Todd flees the Daedalus in a Wraith scout ship.

Plot
After being tracked for several days, a Wraith Hive ship exits hyperspace over M35-117 and transmits a file to Atlantis, which as taken precautionary defensive measures including raising the cloak. After seeing the highly corrupted video file, Col. Sheppard and his team are sent to try and make contact with the Hive via cloaked Puddle Jumper.

However, as they try to establish radio contact, Rodney discovers that there are no life-signs aboard. Curious as to how the ship flew itself to Atlantis, the team lands in the ship's dart bay. Upon securing the, apparently abandoned, ship and making their way to the bridge, they discover the Wraith crew in stasis, with all hands stricken with a disease caused in part by Dr. Keller's gene therapy. The team also notices a series of power fluctuations occurring on the ship, wrecking havoc on the ship's systems.

The team is then joined by Dr. Keller and Major Lorne and his men, which include a team of Marines. One of them, Lt. Williams, stands guard in a remote part of the ship when he hears a noise. Williams investigates, and finds that part of the wall is melting away, revealing a hidden corridor behind it. He radios Lorne (who is with Sheppard) and investigates, and is killed when an un-masked Wraith warrior suddenly reaches out of the opening and grabs him. However, he is not killed by being fed upon, but by being eating to death by the wraith drone's newly activated digestive system. When Sheppard and Lorne arrive on the scene with the another Marine, they find the Lieutenant gone... only his weapon left behind.

Elsewhere, Dr. Jennifer Keller is being challenged to expand her knowledge of Wraith physiology. She discovered that the treatment worked on the Wraith as planned, but when their immune system were at their weakest, a deadly virus became active. However, she has no idea how to eradicate the virus. The pressure is on, and Jennifer candidly confesses a lack of self-confidence to Rodney McKay. The two have begun to grow closer, and he tries to encourage her. However, Keller decides that she can't come up with a cure herself and so, the team decides to revive Todd from his hibernation chamber. Meanwhile, they team notices that the ship's schematics, which they are using to navigate through the ship, are no longer accurate, as new walls are forming and only ones are being destroyed.

Still experiencing an increasing amount of power fluctuations and systems failure, the team doesn't want to take the chance that any more Wraith will inadvertently come out of hibernation due to a subroutine in the ship that automatically revives them. And so, Col. Sheppard tells Rodney to shut down power to all of the active hibernation chambers, effectively killing the Wraith in them. However, Rodney only manages to shut down four out of the five active chambers. This is because they Wraith from the last chamber have already awaken and are now freely roaming the ship, roughly two dozen of them... killing anyone they encounter. Because of this, the team frantically tries to leave the ship. However, one possible escape route to the dart bay has been blocked by a newly formed wall, leaving only one other passage... a passage that has been completely destroyed, leaving a huge gap in the ship.

As the ship continues to loose hull integrity, a massive stress point spanning the entire width of the ship finally fails, splitting the ship in half. However, as the back half remains in orbit, the forward half (in which the team is in) begins to loose its orbit, and descend into the atmosphere of M35-117. With no hope of stopping the ship in time, the team re-enlists the help of Todd. As he makes his way back to the bridge, he quickly gains control of this ship, firing the forward thrusters with all of the remaining power. However, the ship is rapidly descending. Todd then manages to level out the ship moments before it slams into the oceans of M35-117, sending a huge wave out in all directions.

Back in Atlantis, Col. Sheppard (who was rescued along with his team via Puddle Jumper moments before the hive ship completely sank) talks with Richard Woolsey in his office about what to do with Todd, who they now have under guard. After being persuaded by John that Todd is more useful to them being out in the galaxy, he decides to left him leave. As Todd approaches the active Stargate, he has a brief conversation with Sheppard, thanking him for letting him go.

Background
Executive producer Joseph Mallozzi stated in his blog: A mysterious arrival, a difficult dilemma, and the continuation of a storyline introduced in The Queen.