McKay is on a mission with a pilot, Griffin, when they hit turbulence and go down in the ocean. He manages to make contact with Atlantis and Zelenka, and Griffin is awake as well, but they're 1200 feet deep and sinking 20 feet a minute. Worse, the systems go out and the front port begins to crack. They move back into the rear compartment but the door is jammed and Griffin sacrifices himself to close the door manually with McKay inside.
Zelenka briefs Weir and Sheppard and warns it'll be difficult to locate them since they're no longer transmitting. As they prepare a rescue team, McKay tries to overcome his panic and activates the emergency transmitter, but he only has three hours of power and the inertial dampers are on-line and he can't turn them off.
Zelenka and his team are trying to pinpoint the Puddle Jumper's location, while McKay continues to try and save himself and notes he may have a concussion. He needs to rig up a heating circuit as the temperature drops, but it will cost him 20 minutes of power. Sheppard has acquired a winch & grapple system from another expedition and plans to use it to rescue McKay…in two hours. McKay starts hysterically "bargaining" with a nearby whale-like creature, and then realizes he might be able to get the pod to "swim" back to the surface. Then he hallucinates…Samantha Carter, who assures him they'll get him out of there.
The hallucinated Sam is quick to assure McKay that she is a hallucination and he's basically arguing with herself. McKay begins to wonder what else he's hallucinating, and find's "Sam's" reassurances dubious in the extreme. Back at Atlantis, Sheppard suggests they convert the cloaking device into a shield to boost their Puddle Jumper to get that far, although Zelenka is reluctant to go until Weir persuades him.
McKay prepares to use the drive pods to boost himself up and "Sam" advises against it, saying he should trust his team. McKay is reluctant and proceeds with his plan. The Puddle Jumper finally hits bottom and McKay thinks that's good news until "Sam" points out a micro-fissure in the hull.
Sheppard and Zelenka are approaching the area where McKay is, while McKay struggles to repeal the fractures. "Sam" suggests he increase the pressure and he agrees then works to increase the temperature, while berating Zelenka who should have gone on the mission but didn't. Zelenka gets the shield up against the pressure but it's draining too much power. Meanwhile "Sam" strips down to get McKay hot and McKay goes along for a while but he concludes she's trying to distract him and ignores her. "Sam" puts her clothes back on and tries to get him to stop before he endangers himself due to his concussion. He manages to engage power briefly but it uses up too much energy and he only has a half hour left.
Zelenka spots a huge sea creature approaching and advises they stay away, but Sheppard concludes it may be checking out something interesting. McKay is huddled in the cold water and "Sam" tries to reassure him his friends will come. Zelenka and Sheppard find McKay's ship but it's too filled with water to lift with the crane. Zelenka figures out they can extend their shields and hook up. They call up McKay and tell him to open the door, but he wonders if it's another hallucination. With time running out, "Sam" reassures him and he goes for it. He dives down for the secondary release, the water pours out, and Sheppard and Zelenka get him out. "Sam" waves to him as they depart.