The crew of Puddle Jumper One has narrowly escaped the Wraith while on a recon mission to that hostile race's homeworld. The team had discovered that the Wraith hive was not simply within a tree-covered mountain; it was that mountain - and it has now evidently flown off into space. However, the Wraith left behind warriors who attacked them, as well as a scorpion-like parasite that has attached itself to the throat of Maj. John Sheppard - putting him in great pain as it tries to suck the life out of him. Also aboard the spacecraft are Lt. Aiden Ford, Sgt. Markham, Sgt. Stackhouse, Dr. Rodney McKay and Teyla.
As they approach the stargate orbiting the Ancients' planet, the Puddle Jumper's damaged engine pod fails to retract, and the ship gets jammed in the stargate aperture. Horrifyingly, the front half of the ship, containing Markham and Stackhouse, becomes stuck in the 'gate's event horizon, while the other half remains in space. McKay points out that, according to wormhole physics, they have 38 minutes before the 'gate automatically shuts down. The dematerialized fore of the vessel, along with those inside, will cease to exist, and the other half will be severed and sent floating in space with everyone inside exposed to the vacuum of space. The clock is ticking.
At Atlantis, Dr. Elizabeth Weir, in radio communication with the Jumper, mobilizes the Atlantis team. She orders medical officer Dr. Carson Beckett to find a way to remove the parasite before it kills Sheppard, and orders the 'gate room quarantined in case the creature must be brought in. Czech scientist Dr. Zelenka works up a simulation in Puddle Jumper Two, hoping to isolate the correct control pathway that will fully retract the engine pods - and not, for instance, open the rear hatch to the vacuum of space. Another scientist, Simpson, recommends closing the bulkhead door, so that if the ship is severed, the aft might work as a lifeboat until another Jumper can be sent on a rescue mission. McKay is already ahead of her on that.
Yet another scientist, Kavanagh, points out that with the cockpit controls interrupted and the pod damaged, the main drive could overload - and the subsequent explosion might not merely destroy the Jumper but could send burning fragments through the stargate with bomb-like force. To prevent this, he recommends activating the stargate shield - dooming all aboard Jumper One. Weir quickly confers with the other scientists, determines the risk is slim, and orders the 'gate kept open.
Beckett has Teyla and Ford pour everything in their emergency medical kit onto the parasite to see if anything will cause a reaction that makes the creature let go. Nothing works, and when water is tried, the creature causes Sheppard even more agony. Sending Sheppard across the event horizon, where he'll remain in suspended animation until the ship passes completely through the stargate, is out of the question: If a few drops of water caused such a violent reaction, who knows how the creature will react to 'gate travel?
Sheppard suggests using their portable defibrillator to stop his heart. The parasite, detecting no life, might stop feeding. Then they can zap Sheppard back to life. It works: The bug detaches from Sheppard. Ford wraps it in his jacket and shoots it. But attempts to shock Sheppard back to life fail. The only hope is to send him through the event horizon. Teyla goes as well, in order to pull Sheppard through.
With only two minutes left, McKay, with Zelenka's radioed help, gets both pods retracted. But the ship still isn't moving, because the drive shut down before they entered the stargate. With one minute left, Kavanagh realizes that blowing the rear hatch will thrust the jumper through the 'gate. McKay goes through the event horizon and Ford blows the hatch, holding on for life as the air is sucked out of the ship - taking the creature, which has just come back to life, with it. Puddle Jumper One goes through the 'gate and arrives at Atlantis, where a medical team on standby resuscitates Sheppard.