Infection

"Infection" 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, Lt. Colonel John Sheppard's team discovers that its crew has been stricken with a disease they helped create.

Previously on Stargate: Atlantis
Lt. Colonel John Sheppard's team makes contact with Todd a board his Hive ship in the hopes of stopping the Asurans. Dr. Jennifer Keller and Sheppard's team make a proposal to Todd; Keller has found a gene therapy in Michael Kenmore's database that should free the Wraith from their need to to feed on Humans. Later, Todd and a delegation arrived on board the Daedalus to go forward with Keller's gene therapy. However, Todd witnessed two Wraith cruisers getting destroyed the second they go into hyperspace. He accused the Atlantis expedition of getting hold of the Attero device. In anger, he stunned the crew and locked down the ship, as well as sending more Wraith to the ship. In the hopes of destroying the Attero device, Todd attempts to crash the Daedalus into Janus' research outpost on M6H-987 before fleeing the Daedalus in a Wraith scout ship. However, Sheppard, with the help of a Traveler generational ship, creates a hyperspace window around the Daedalus, saving it moments before destruction.

Plot
After being tracked for several days, a Wraith Hive ship exits hyperspace over M35-117 and transmits a file to Atlantis, which has taken precautionary defensive measures including raising the cloak. After seeing the highly corrupted video file, Lt. Colonel John 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, Dr. Rodney McKay 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 that the Wraith crew is in stasis, with all hands stricken with a disease caused in part by Dr. Jennifer 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 Keller and Major Evan Lorne and his team. 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 eaten by the wraith drone's newly activated digestive system. When Sheppard and Lorne arrive on the scene with another Marine, they find the Lieutenant gone... only his weapon is left behind.

Elsewhere, 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 was at its weakest, a deadly virus became active. However, she has no idea how to eradicate the virus. The pressure is on, and Keller candidly confesses a lack of self-confidence to McKay. The two have begun to grow closer, and he tries to encourage her. Meanwhile, the 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 other ones are being destroyed... literally melting away.

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 during power failures. And so, 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, and the team stranded.

McKay then comes up with a theory as to the ship's problems: Because Wraith ships are organic and repair themselves, it is possible that the ship is repairing itself incorrectly. However, because the problems with the ship are too serious and lacking the knowledge to properly fix it, McKay persuades Sheppard to revive Todd. It is Todd who discovers the reason for the ship's problems: during hibernation, fluids are exchanged between the Hive Ship and the occupant of the hibernation pod. Because the Wraith in the pods were infected with the virus, the ship became infected with it as well, leading to the power failures and malfunctions.

To avoid the constant threat of Wraith sporadically reviving, Sheppard tells McKay to disable the safety protocols in the hibernation chambers. If a Wraith revives, instead of releasing it, the pod will stay sealed, suffocating its occupant. However, McKay only manages to alter four out of the five active chambers. This is because Wraith from the last chamber have already awoken and are now freely roaming the ship, roughly two dozen of them, hungry with their newfound ability to eat. Sheppard, Ronon Dex, Teyla Emmagan, Lorne and the remaining marines quickly assemble into teams to exterminate them, and soon engage in close-quarters combat as they eliminate as many of them as possible.

Meanwhile, Todd works with Keller on a way to cure themselves of the virus. He ultimately realizes a way to do just that. Long ago, a method was devised to restore a Wraith to near perfect health. Hardly any Wraith survive the process, but as he is beyond hope, he is willing to try. The solution is to be fed upon by an Iratus bug. He then asks Sheppard to take the Hive Ship into hyperspace to a planet with Iratus bugs on it. However, not entirely trusting Todd, and questioning the ship's structural integrity, he says no. Todd, who is now incredibly angry, is taken away to a holding cell.

During this time, the rest of Sheppard's and Lorne's team are battling the remaining wraith warriors. However, as the ship is quickly losing integrity, Sheppard orders them back to the bridge.

As the ship continues to lose hull integrity, a massive stress point spanning the entire width of the ship finally fails, splitting the ship in half moments after the teams fighting the Wraith make it to the front portion of the ship. As the back half remains in orbit, the forward half containing the Atlantis team begins to lose its orbit, and descends 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 the 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, 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, now under guard. After being persuaded by John that Todd is a powerful ally and is more useful to them being out in the galaxy, he decides to let him leave through the Stargate to seek out an Iratus bug. As Todd approaches the active Stargate, he has a brief conversation with Sheppard, thanking him for letting him go, saying he will remember what Sheppard has done for him.

Notable Quotes
Sheppard: Well, the Wraith have thrown us a little curve ball here. We've got no life signs on board. We think they're hibernating.

Woolsey: Why would they do that.

Sheppard: Well, that's what we'd like to find out, but it means boarding the ship.

Woolsey: Are you sure that's wise? What if it's a trap?

Sheppard: Well, if it is, it's a pretty lousy one. If they ambush us, you can still take 'em out from down there.

Woolsey: Sacrificing your lives.

Sheppard: I'm flattered you think Todd would go to so much trouble to kill me. Look, taking out a hive ship is always a good idea as far as I'm concerned, but we did come all this way, and … got all dressed up.

Todd: I did not think you would come.

Ronon: What are friends for?

Keller: I just feel like I'm in over my head.

McKay: What are you talking about?

Keller: I look at you, and Colonel Sheppard, the rest of the team … and you guys are so used to making decisions that affect the lives of thousands, and even millions, of people. I'm not so used to having the fate of the galaxy hanging in the balance.

McKay: Oh, that. You get used to it. Helps to have a massive ego.

Keller: The disease is in the ship?

Todd: It is the only explanation that makes sense.

Sheppard: All right, if you say so.

Keller: How is that even possible?

Todd: During the process of hibernation, there is a continuous exchange of fluid between Wraith and Hive.

(John looks disgusted.)

Todd: The disease must have been transmitted in this manner.

Sheppard: Great, so we're flying around in a giant tumor.

Sheppard: Get up.

Todd: You can't quite leave me be.

Sheppard: I don't have time to play games, you know what that shaking is?

Todd: Oh I can guess.

Sheppard: We've lost orbit. We're entering the atmosphere which means in a few minutes we're going to slam into that Planet

Todd: A quick death will be a welcome reprieve!

Sheppard: Oh I didn't think you were such a quitter.