During the first test flight of a Puddle Jumper that Dr. Zelenka has repaired, the small ship abruptly crashes and sinks into Atlantis's ocean with Dr. McKay and the pilot, Griffin, on board. Moments later, mounting water pressure cracks the Jumper's windshield. Griffin sacrifices himself to seal a horrified McKay into the relative safety of the windowless rear compartment, seconds before the windshield gives way.
McKay is now utterly alone - and still sinking. He manages to activate an emergency beacon, turn up the heat, and fix the carbon dioxide scrubbers. Every action he takes, however, costs power - power he desperately needs to stay alive. He's already close to panic when a strange whale-like creature starts taking an interest in the Jumper.
But the creature's swimming gives McKay an idea. If he can power up the Jumper's drive pods, perhaps they can propel him to the surface. Suddenly, however, an unexpected visitor joins him: Col. Carter, from SG-1. McKay, shocked, accuses her of being a hallucination, and she cheerfully agrees. The concussion he received in the crash, plus the stress he's been under since, has provoked his subconscious to summon this unusual form of help.
Unfortunately, McKay and Carter - or McKay and his subconscious - have a fundamental difference of opinion. He believes he must risk activating the drive pods, while Carter argues that this will only waste the last of his precious power. She wants him to remain calm and trust his teammates to rescue him. McKay, by contrast, blames Zelenka for the crash and has no confidence in the Atlantis team's ability to save him - especially without his genius to help them out. As water starts leaking into the Jumper, he insists on pursuing his risky plan.
On the surface, however, Zelenka has worked tirelessly to narrow down the Jumper's probable location, and now has joined Sheppard on a second Jumper for a dangerous rescue mission. He modifies the Jumper's cloak to act as a tenuous shield against the water pressure as Sheppard submerges the vehicle and begins the search.
McKay defies Carter's advice - and her creative attempts to distract him - and fires up the drive pods. They activate briefly and then die, proving Carter right and leaving McKay with barely enough power for another half hour. His survival is now up to his friends - and only his hallucination believes they're really on their way, let alone that they can arrive in time.