How's this for credibility? Weir is dead. Stay out of my way, or McKay will join her.
— Acastus Kolya
Of course Kolya didn't really shoot Weir, but Sheppard doesn't know that. After vowing to avenge her Sheppard heads back into the city as Koyla takes Weir and McKay to the grounding station so that Rodney can repair it before the full force of the storm hits. Rodney is less than pleased with the damage that's been done and makes a big deal out of how much work it'll take to repair it, Weir ad-libs some technobabble to give Rodney an excuse to work slowly and buy Sheppard time.
Over on the mainland, the puddle jumper containing Teyla, Ford and Beckett has entered the eye of the storm, allowing them to fly straight up out of the atmosphere and over the turbulent storm front.
Back in the city Sheppard has been busy, in between taking out Genii guards he deactivates the generator that powers the control tower, meaning that the Genii can no longer use the city's sensors to track him. As the Genii make arrangements to guard the remaining generators the grounding station goes dark, looks like he's already got that one too. With no power, Rodney cannot repair the station.
The puddle jumper arrives in the jumper bay and Teyla, Ford and Beckett move out into the city to assist Sheppard. They only have a lifesigns detector with them which cannot differentiate between individual signals so they cannot determine which dot is Sheppard, but Ford isn't worried.
In the control room, the Stargate has just activated and the Genii are expecting 60 soldiers to come marching through. Until Sheppard sneaks in and punches out the lone technician manning the controls, just as the first 5 soldiers come through the gate shield is suddenly raised. Shouting 'Stop him' does not have the desired effect and Sheppard escapes back into the corridors. McKayand Weir both insist that they have no idea how to lower the shield as we are treated to the sound of 55 Genii soldiers going splat. The gate shuts down and Koyla asks about his son, who was one of the 60 soldiers due to arrive. The news that he didn't make it does not go down well.
Kolya delivers an ultimatum, either Sheppard returns the components he swiped from the generators, or Weir dies. For real this time. Sheppard sees no alternative and doubles back to the generator that feeds the grounding station. Just as he is about to restore power he is jumped by two Genii guards who demand that he drop his weapons and remain still. His complaint that Kolya will execute his friends if the generator is not repaired is ignored as the guards refuse to listen to him. Fortunately, the cavalry arrive just in time, Teyla and Ford take out the two guards and Sheppard re-activates the generator, the grounding station lights up, Kolya holsters his gun and McKay is ordered to continue repairs.
The repairs complete, McKay successfully de-activates the grounding station and insists that they need to get back to the control room ASAP. With the grounding stations de-activated, every bolt of lightning that hits the city will have nowhere to go and will instead swirl around, electrifying every corridor in the city. Team Sheppard also know this and head back too, but they are being tailed by Sora, determined to avenge the death of her father by killing Teyla.
Sheppard and Ford put together a plan to retake the gate room while Teyla and Beckett head off together on their own task. Unfortunately, Sora takes this moment to strike, incapacitating Beckett and forcing Teyla into a knife fight. McKay gets back to the control room and initiates his program which should channel the lightning, soon to be zapping around the city, into the shield generator.
Diverting power, NOW!
Nothing continues to happen
Oh dear, seems that the long shot chance at saving the city has failed, Rodney's program doesn't work and there is now no way to protect the city from the full force of the storm. Kolya decides to cut his losses and retreat through the gate, taking Weir and McKay with him. As they all file through the gate Sheppard and Ford attack. In the confusion, McKay makes a break for cover as Kolya uses Weir as a human shield. He backs toward the gate and mocks Sheppard. Surely he won't risk hitting Weir.
Kolya takes a single bullet directly to the shoulder, drops Weir and falls backwards through the gate. Weir is shocked, but she'll be OK. Rodney runs to a console, his earlier failed attempt at saving the city was just a ruse. There's a tsunami heading their way which will obliterate the city in a little more than 2 minutes, Sheppard instructs him to wait 2 minutes for Teyla and Beckett to make it back to the control room so they will not be killed when the corridors electrify. Teyla wins her fight but refuses to kill Sora, just as Sheppard comes over the radio and warns her that if they are not back in the control room within 2 minutes they will all die. Teyla drops her weapon and runs. An angry but defeated Sora runs after her.They return, carrying Beckett, just in time as Rodney activates his program. Lightning courses through the cities corridors and Rodney casually greets Beckett as the power reaches the necessary levels.As a massive tidal wave approaches the outer edge of the city the shield activates and the wave impacts harmlessly. We cut to the next day, the city is safe and the evacuated personnel are returning, Sheppard asks if he can book the next storm off.