A mentally limited Rodney McKay speaks to the camera on Day 15 as Dr. Keller records him. McKay talks about how he's losing his intelligence and Keller insists they're trying to fix it. McKay calls out for John. Jeannie Miller cuts off the tape and wants to know why they didn't notify her sooner, and Keller apologizes for not identifying the symptoms sooner. Woolsey warns that they were concerned she wouldn't get there in time to say goodbye.
Sheppard explains to Jeannie what happened.
Sheppard took his team on a mission to check in on a scientist who has lost contact with Dr. Nickels and his team. Woolsey prepares to leave when an unscheduled gate activation occurs. Sheppard signals to tell them the local area is flooded with cold water and Atlantis needs to send a Jumper through. However, Sheppard's team can't disengage the gate because of the water. While they wait for it to disengage automatically, they try to contact the research team. McKay collapses and the team comes back later, waiting until the Jumper has found the research team. Sheppard checks up on McKay in the infirmary but Keller says that he checks out fine but is keeping him for observation.
Keller prepares McKay to meet with his sister. He's barely able to remember his name and a crying Jeannie steps outside. Ronon tries to comfort her and explains there's somewhere he can take McKay so he'll be okay long enough to say goodbye.
As Keller goes over the tapes McKay made of his mental deterioration, Jeannie comes in and asks for an explanation. Keller reveals that a parasite has infiltrated McKay's mind and even stasis doesn't slow its spread. Keller notes that McKay was suffering from a viral infection that lowered his resistance so he caught the parasite. Ronon has recognized the disease as "Second Childhood" but Keller insists on treating it. Keller again apologizes for not seeing the symptoms.
McKay is eating dinner and invites Keller to join him. He's exceedingly personable.
Keller notes that if McKay hadn't been so chipper, she might have noticed the symptoms sooner. Jeannie wonders why Keller won't let Ronon take McKay to the Shrine where he might revert.
Ronon explains that he saw the Shrine as a six-year-old and witnessed his grandfather recover for a day and then die with honor. Woolsey is skeptical and notes the planet has a Wraith camp on it. Woolsey explains that his father had Alzheimer's and had one moment where his father recovered enough to recognize him. Ronon insists it isn't the same and offers to take McKay, feeling he owes him. Teyla volunteers as well and Sheppard says they need a plan, but Keller won't give her permission until they talk to McKay. They go to see McKay and Ronon tries to explain. McKay agrees but Keller insists that he get a full explanation. She warns that if he leaves, she can't treat him. McKay is unable to decide and Keller refuses to grant permission to take him to the Shrine.
Keller doesn't believe the damage is permanent and insists on trying to find a way to remove the parasite. Jeannie takes on the decision of next-of-kin and insists on moving her brother to the Shrine.
Sheppard prepares to depart and Woolsey asks him to pass on his own goodbye. They board the Jumper and send a MALP through. The Wraith open fire as the MALP spreads smoke and the cloaked Jumper goes through the Stargate and gets clear.
McKay runs to Sheppard's quarters in a panic after he realizes that his friend left. He's frightened that he's slipping away but Sheppard manages to calm him down and they go out on the pier to share a few beers. McKay wants to say goodbye now but Sheppard insists he'll remind McKay no matter what.
They arrive at the Shrine, which is behind a waterfall. They enter and wait, while Keller picks up faint energy readings. Teyla finds a tablet which is the source of the energy readings and they get the terrified McKay next to it. He then recovers all of his mental acuity and doesn't remember anything that's happened. He demands to know why he isn't in the infirmary and Jeannie explains that the effects only last a day. McKay insists on staying but Ronon warns that it doesn't work that way. McKay's furious that they're torturing him because he's already come to grips with the situation, and that he'll revert again. McKay finally accepts the situation but Keller wonders how the cave worked. They go over the power readings and McKay determines that the energy readings match those of an Ancients power device. Keller tests her theory by taking McKay out of the cave and the parasite expands again. They get McKay back into the cave and Keller concludes the radiation causes the parasite to contract. Keller can operate on him while it's contracted… but they can't move McKay out of the cave.
Keller needs equipment from Atlantis but Sheppard warns the Wraith won't fall for the same trick. He asks her what the bare minimum equipment is that she needs and he takes Keller back to the Jumper to scavenge what equipment they can from the ship's toolkit. Sheppard suggest she use a life sign scanner to find the parasite but Keller insists that there's nothing they can do. Sheppard says that if she doesn't operate, McKay is dead.
McKay is less than thrilled at the idea but has no choice but to consent. Keller renders him unconscious with anesthetic and begins the operation. Keller opens a hole and then sees that the parasite is moving out now that it has an escape route. The parasite emerges from McKay's skull and Keller throws it away where Ronon can kill it.
Back on Atlantis, McKay recovers in the infirmary with Jeannie at his side. He thanks Keller for saving him and admits he was scared. Keller goes to get him some food. Keller reviews the tapes that McKay recorded, including the one where he admits that he loves her