This episode is part 2 of 3; it is preceded by “First Strike” and followed by “Lifeline”.

Jennifer Keller and a medical team takes a gurney with an injured Elizabeth Weir to the infirmary. However, on the way, Weir flatlines. Keller tries to revive her, and soon arrives in the infirmary to operate on her, but they have to revive her first. Ronon Dex is also in the infirmary, demanding a doctor to remove a piece of glass on his chest. Meanwhile, in the control room, Rodney McKay works furiously to restore the Stardrive, and Subspace communications, since they were all damaged by the brush with the beam. McKay discovered that the power conduits are damaged, which prematurely deactivated the stardrive. They work on repairing them. Back in the infirmary, Weir has flatlined for two minutes. She’s suddenly back in V-fib, so Keller uses the defibrillator, which bought her back to life. Back in the control room, McKay tells John Sheppard that they are draining too much power, and will be lucky if they could survive the night.

A while later, Sheppard approaches McKay, and tells him that since Weir is incapacitated, Sheppard is in charge, and wants McKay to keep him in the loop. McKay tells him that he deployed some teams to patch up the damaged conduits. They have made significant progress in fixing them, and they would have at least an extra hour of power. However, an alarm sounds. They discover that the shield is collapsing, and McKay can’t stop it. Sheppard warns a team led by Matthews to finish the work and escape to the central tower. The team attempts to do so, however, the shield is collapsing too quickly. The team almost makes it, but the artificial gravity shuts down, and the shield passes the helpless team. In the control room, the team watches helplessly, as they see the bio signatures fade away. Sheppard orders the other teams not to take too long.

Carter and Lee in the almost operational Midway station.

Meanwhile, in the almost completed Midway space station, Samantha Carter and Bill Lee work on activating the artificial gravity, when Bill vomits due to the weightlessness, but insists on staying to get the gravity on. Suddenly, the Pegasus Stargate activates. Colonel Abe Ellis contacted her to inform her that Atlantis has left Lantea, but did not arrive on M12-578, since Atlantis was supposed to beat them there. Ellis then took the Apollo to the nearest planet with a Stargate and told Carter the situation. Ellis then decides to head back to 578 and dial back in one hour.

Back in Atlantis, Ronon checks up on Weir. There, he learns that Weir is in critical condition, her brain is swelling and if it continues, then they have to perform a decompressive craniectomy. Meanwhile, McKay tells Sheppard that the teams have finished, and in order to save more power, the shield has to collapse to cover only the central tower, which Sheppard authorises. The shield quickly transforms to a cigar shaped bubble surrounding the control tower. Back in the infirmary, Keller learns that Weir’s brain is swelling to dangerous levels. Keller has to stop it, so she performs the craniectomy, which does stop the swelling.

McKay brings the team two pieces of good news. A), they’re no longer lost, but the subspace communications are beyond repair. B), the stardrive wasn’t damage, just that the conduits were damaged, and Radek Zelenka is making excellent progress, by using secondary conduits to patch up the damaged ones. Sheppard then pops into the infirmary, where Keller gives him a diagnostic of Weir’s condition; she has six broken ribs, one of which punctured a lung, but no spinal damage. However, her head got knocked around badly, causing substantial brain damage. Meaning that even if she will revive, she’ll never be the same Elizabeth again. This news puts Sheppard on an uneasy position.

In the ZPM room, Zelanka tells McKay they will soon finish repairs to send Atlantis to M12-578. However, there’s a problem, the city is on a collision course with an asteroid belt, which leaves them an ultimatum. If they take the shields back to its original shape, the power drain would lose any chance of restoring the stardrive. If they remain, the city would fall apart. With the chair room out of reach of the shield, Sheppard has one plan left. He calls in everyone with the ATA gene to fly Puddle Jumpers to make a clearing for Atlantis to go through unscathed. However, most of the people rarely flew Jumpers and had little experience. However, Sheppard has complete faith in them. They fly away and get into formation until they are in firing range of the asteroids.

McKay chases after an asteroid zeroing in on Atlantis.

The pilots start firing drones into the asteroids. Despite little experience, the pilots managed to have wiped out several asteroids. After the half way point, McKay and two more Jumpers pick off some stragglers, particularly the big asteroid about to hit Atlantis, which is intercepted by McKay. The other Jumpers make it through and return to pick off the stragglers. In Atlantis, they feel the effects of some smaller pieces hitting Atlantis. The city sustains multiple hits, but went through the field, putting everyone into relief. The Jumpers return, with McKay’s shock that the plan worked. However, he is called to more bad news; some of the asteroids that made it through Atlantis has damaged some of the stardrive’s control crystals. They have to repair it.

There is a catch, the crystals are outside the shield, meaning they would have to make it there in space suits, and would have to work fast, before the power levels will dip too low to get the stardrive online again. Sheppard and Zelenka ready their space suits. Meanwhile, McKay gets a visit from Keller, who gave him an idea to get Weir back to her original self, by reactivating the nanites she was infected with by Niam a year ago. McKay tells Sheppard about the plan, only to tell him not to, since Weir wouldn’t want that to happen. However, McKay works on a plan to reprogramme them in a way that it will not be a threat to her.

Back in the Midway station, the artificial gravity is now online, where Carter and Bill work on a way to contact Atlantis. Bill proposes an All-gates bulletin, which Carter declines, due to its numerous flaws.

Sheppard and Zelenka walk through the exposed hallways. However, on the way, they find a big gap between them and the control crystals. Sheppard plans on a space jump, by pushing Zelenka and using his inertia to pull Sheppard across the gap. It works and Zelenka starts on replacing the damaged crystals. However, a micro-asteroid cuts through Zelenka’s uniform and through one of his legs. However, Zelenka insists on continuing.

In the infirmary, Ronon comes up to Weir and thanks her for letting him in Atlantis, because he would be dead if he carried on as a runner. However, her vitals spike. Keller pushes Ronon away and tells McKay to activate the nanites or she’ll die. Despite not finished, McKay gives her the activation codes.

Zelenka finishes replacing the crystals. However, when Sheppard tells Teyla, she tells them that the power levels have dropped below the minimum level required to jump. They have 30 hours before the shields completely fails, which will kill them all. But there’s another problem; Sheppard finds out about Weir, and snaps at McKay. He orders him to terminate the nanties, which McKay refuses. But Weir has just awakened from her coma and wonders what is going on. They put the room Weir is in placed in quarantine. Weir tells Teyla that reactivating the nanites is a bad idea, as they have no idea what she went through last time.

In the Midway station, Carter has an idea. They use the Apollo to make several little jumps and use the Long range sensors to find Atlantis. However, since several thousand jumps are required, Carter plans on augmenting the ship’s sensors. They plan to dial to the Pegasus Galaxy.

Back in Atlantis, the team tries to figure out an alternate plan to save Atlantis. Zelenka proposes they override the city safeguards and try to activate the hyperdrive with their available power. However, doing so means there is a 50/50 chance the hyperdrive will either work, or destroy the city. Sheppard rejects the plan as it is too dangerous and insists they try something else. McKay and Zelenka then realize they can use the hyperspace-capable Jumper that McKay designed when he was once physically augmented. Though it can’t travel very far, the Jumper does have enough power to jump to a nearby planet and return. McKay and Zelenka plan to take the Jumper to a nearby planet. On the screen, McKay finds M7R-227, which has several ZPMs. 227 is actually the Asuran homeworld, and McKay proposes a heist to steal a ZPM.

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