The city of Atlantis is adrift in deep space after narrowly escaping a Replicator assault. With Elizabeth Weir badly injured, John Sheppard assumes command of the city, and Jennifer Keller, Atlantis's new chief medical doctor, fights to keep Weir alive.
Meanwhile, Rodney McKay and Radek Zelenka discover that, although Atlantis's Z.P.M. power source is functioning, the Replicator attack damaged the main conduits that carry power into the city. The power being pumped through these conduits is hemorrhaging into space, and soon the Z.P.M. will be drained.
Worse, in an effort to save power, the city's automated systems are relentlessly decreasing the size of Atlantis's shield. Several people perish in the vacuum of space after the shield abandons their part of the city.
Soon after McKay and Zelenka initiate patchwork repairs on the conduits, an asteroid field looms up on the city's sensors. Without propulsion or shields, Atlantis will take a terrible beating.
Sheppard herds all available pilots - including McKay - into the Jumpers, then leads his small armada out into the asteroid field to blast open a path for Atlantis. The inexperienced pilots overcome their nerves and triumphantly prevent all but a few small asteroids from impacting the city.
Unfortunately, Atlantis just can't catch a break. An overlooked asteroid damages one of the hyperdrive's control arrays, dealing the city another crucial setback. Sheppard and Zelenka space-walk out to the exposed array to fix it. A microscopic asteroid rips through Zelenka's leg like a bullet, but with Sheppard's support, the scientist heroically finishes his repairs.
Meanwhile, Keller approaches McKay with a strange proposal. Weir is near death, and Keller believes only one thing can save her: the inactive nanites that were left in Weir's body by a failed Replicator attempt to take her over. If McKay can reprogram the nanites to repair Weir's injuries without summoning their dangerous cousins the Replicators, Weir might survive. Sheppard opposes the plan, but McKay and Keller can't bear to let Weir die. They activate the nanites.
All this time, the city has continued to leak power like a dripping faucet. In the end, despite everyone's hard work, they fail to finish all the repairs before the power levels drop too low to initiate the hyperdrive. They're trapped in space aboard their dying ship. Then, suddenly, Weir awakens. The nanites have healed her and now form part of her body. On the heels of this apparent success, McKay has a daring idea: They might be able to fly a Jumper to the nearby Replicator homeworld and steal a Z.P.M. It's a long shot, but given their grim situation, Sheppard's inclined to take the risk.