Teyla visits the infirmary with her son Torren. She tells Dr. Keller that she has walked half the city and back trying to keep him asleep. She mentions that she has visited Kanaan and that he is himself again. She thanks Dr. Keller for her treatment of Kanaan, and says that she plans to ask Woolsey to let him and the others stay at Atlantis. Dr. Keller used Dr. Beckett's retrovirus to revert the hybrids, and she is trying to come up with a cure for Beckett's tissue degradation so they can remove him from stasis. Torren wakes up and starts to cry and Teyla resumes walking.
The Daedalus arrives from hyperspace. Sheppard and others are waiting in the control room as Woolsey arrives an dasks for copies of everyone's reports. Sheppard notes that Woolsey didn't make any attempt to give an arrival speech to his new team.
That night, Dr. Keller is dozing at her computer and wakes up to find her hand cover in a mucus-like substance. She is concerned, but washes it off and doesn't say anything to her staff. She then goes to her quarters to sleep.
The next morning, the team arrives for their briefing and Sheppard believes that since Carter eliminated numerous threats, the IOA has jumped at the chance to put a civilian in charge. Woolsey enters and congratulates them on their victory over Michael, but they mention that Michael apparently escaped in a Jumper. Woolsey refuses to order a search for Michael and asks Keller how the hybrids' rehabilitation is progressing. Keller, distracted, finally reports that the retrovirus treatment has been a success and has left no lasting ill effects. Teyla wants to know when the hybrids will be released but Woolsey is concerned that they're enemy combatants. He then asks why Keller is devoting so much attention to Beckett's condition and she says she has come up with a serum but doesn't want to remove Beckett until she knows it's safe. He suggest that she make a decision one way or another so she can get back to other matters.
Keller prepares to remove Beckett from stasis then administers the serum and takes him to the infirmary to monitor him for cellular degradation. Later, Beckett regains consciousness and Keller assures him his condition is stable. As she leaves, Sheppard advises her to get some rest. She goes to her quarters and takes a pill to get to sleep. The next morning, Beckett admires the city as Rodney mentions that Beckett will be sent back to Earth later that day to be monitored in a hospital. Teyla calls Rodney for help, saying that Keller didn't show up for breakfast four hours earlier. She has Rodney override the door controls and they go into find Keller unconscious and covered in an alien substance.
Beckett notes that he's seen something similar in one of Michael's labs and the tendrils have attached themselves to both her body and the bed. The doctor takes command, having her put in isolation. Sheppard gives Woolsey an update, and Woolsey is concerned that Beckett is in charge because of his condition. Beckett tries to cut some of the thinner strands of the alien away from Keller but she crashes and they are just able to stabilize her. Woolsey meets with Beckett to tell him he still has to leave in one hour to receive treatment. Beckett insists on staying and convinces Woolsey to keep him on Keller's case for now. Sheppard mentions that Woolsey's decision isn't exactly by the book, and Woolsey warns him not to get used to it.
Beckett has found an alien pathogen in Keller's blood and suspects she may have become infected when she went to rescue Rodney and the others from Michael's collapsed facility. Keller wakes up and they discover that the alien growth has spread further, almost entirely covering Keller and some of the quarantine chamber. Keller starts talking to herself then explains the substance on her hand, but can't remember why she didn't report it or run a scan. Beckett warns Woolsey that the substance is doubling its mass every several hours, and that everyone who was on Michael's planet has tested positive for the pathogen.
Woolsey has everyone infected confined to quarters, although none of them are showing signs of infection yet. Beckett completes his analysis and explains it's a biopolymer that is creating an outer shell similar to the hull of a Wraith ship. The substance doesn't register on their life-sign detectors and they've discovered it's spreading throughout the base, converting material as it goes and siphoning off the base's power. They shut down the power to slow its growth. However, Rodney believes they've made a wrong decision: without the electricity, the pathogen will move to the ZPM power conduits. Teyla passes on Rodney's advice but they note that the pathogen can affect the host's mental processes. Woolsey orders them to assemble a team to conduct a visual inspection since they've lost sensors. Beckett is working on a virus to attack the pathogen, but they have no way to eliminate the polymer itself.
Teyla and Zelenka take a team to locate the spread of the polymer and find it attached to the power conduits. Zelenka tries to scan it and it grabs him with a tendril, knocks him to the floor, and tries to attach itself. Teyla arrives to shoot off the tendrils and they retreat. Beckett concludes the pathogen is intelligent because it's using Keller's mental processes to identify and deal with threats. He has the virus ready and figures it should sever the connection, but it's never been tested. Woolsey needs someone to step right up to Keller to administer the virus. He says that they may need to kill Keller using drones but the alternative is to risk their lives. Sheppard volunteers to let them test the virus on him. Beckett places Sheppard in restraints and injects the virus. Sheppard goes into violent convulsions while Woolsey has the staff cut off the ZPM power conduit. Sheppard flat-lines and they manage to revive him. Beckett confirms that the pathogen in Sheppard's blood has been eliminated and Ronon and McKay all volunteer to administer the virus to Keller. Woolsey doesn't trust Rodney and Ronon but Beckett explains the pathogen is less likely to attack someone infected.
They teleport Ronon as close to the infirmary as they can and he proceeds on foot. Sheppard gets word of the plan as Ronon makes his way through the tendrils of the pathogen. He reaches a point where the corridor is complete blocked and wants to shoot his way through, but Beckett warns him against it. Sheppard realizes things are going to go wrong and grabs more of the virus. Ronon has no choice but to start shooting, but the tendrils quickly subdue him, choking off his air supply, and the rest of the team loses contact with him.
Sheppard arrives in the control room and tells the team to turn on the power and open a channel to the isolation room. He tries to get through to Keller, but the pathogen responds, saying Dr. Keller is no longer present. It says that it is not yet complete but will eventually have a designation. Sheppard tells Beckett to stall for time while he powers up a Jumper. He crashes straight into the isolation room and makes his way to Keller. Tendrils are everywhere - covering the floor, coating the walls, and dangling from the ceiling. Sheppard carefully injects the virus into Keller's neck and she suddenly regains consciousness. The tendrils move against Sheppard and one stabs him in the stomach. Sheppard drops to his knees. He prepares to shoot Keller but she passes out and the tendrils go limp. Woolsey requests a status report and Sheppard breathlessly says they had better come and get them.
Later, a recovered Keller comes to visit Sheppard in the infirmary and apologizes. When Sheppard states that he now has two doctors looking after him, Beckett says that he must still return to Earth that day. When Sheppard and Woolsey are alone, Woolsey admits to Sheppard that his superiors have gone over his report which showed he broke at least half a dozen protocols on his first day of duty. Sheppard tells Woolsey that if he had gone by the books, Keller would be dead, and Woolsey notes that IOA has agreed with him and dropped the matter. Woolsey wonders if he can lead Atlantis if the rules don't apply, and Sheppard shakes his hand and says: "Welcome to the Pegasus Galaxy."