Sheppard: In the cockpit, on the left.
McKay: The cockpit is regrettably demolecularised at the moment.
The episode begins In Medias Res
with the damaged Puddle Jumper fleeing toward the Wraith space gate, while Sheppard lies twitching on the floor with some kind of funky alien bug thing attached to his neck. Due to some damage to the ship, however, the engine pods do not retract, and they get stuck halfway through the Stargate. And due to an entirely new explanation of wormhole physics, this means that not only will the back half of the ship be exposed to hard vacuum when the gate shuts off thirty-eight minutes from now, but the front half totally refuses to re-materialize on the other side, and will be lost in limbo forever. Oh yeah, and Sheppard's got a thing on his neck.
Weir sets a team of scientists to come up with potential solutions given equipment lists and the back half of Jumper 2, Apollo 13
style. McKay fiddles with stuff on their end, while Teyla and Ford (with the help of Dr. Beckett) try pouring various chemicals on Sheppard's bug to get it to roll over and die. They do discover its weakness - salt water - but instead of giving up gracefully it reacts by strangling Sheppard for everything it's worth. What's worse, it seems to posses the Wraith's ability to heal itself by sucking the life out of its host. What's even worse than that, they're pretty sure that gate travel will instantly kill Sheppard if he's still got the bug on him when he goes through.
The only thing for it is to kill him. Ford uses the emergency defibrillators to stop Sheppard's heart, convincing the creature to give up and leave of its own accord. It works, but unfortunately, they can't get his heart started again afterwards, so Teyla drags him through the gate to keep him preserved until they get back to Atlantis. McKay finally manages to press the right sequence of crystals to retract the engine pods - which does nothing, since the Jumper has no forward momentum, and so just sits there. With just seconds to spare, Ford blows the back hatch, letting the explosive decompression propel them the rest of the way through the gate (and conveniently blowing the bug out into space).
Dr. Beckett's medical team successfully revives Sheppard, and there is much rejoicing.
Joe Flanigan (John Sheppard) once said in an interview that this was one of his least favorite episodes.
It is also noteworthy that this is the first time in the Stargate franchise that defibrillators do anything at all.