McKay manages to convince Kolya not to kill him and Weir in case they need to deal with another emergency. Kolya reluctantly accepts his argument but warns Sheppard to stay out of their way and lies that Weir is dead. He then sends more men after Sheppard, but Sheppard is able to kill three of them. Kolya also forces McKay and Weir to work on the damaged grounding station.
Ford, Teyla, and Beckett are still stuck on the mainland in the Puddle Jumper when the eye of the storm passes over them. Taking advantage of the lull, they fly up out of the storm and head for Atlantis. Weir and McKay meanwhile try to delay repairs. Kolya decides to call for reinforcements – 60 or more men to come through and back up his strike team. Sheppard disables the generators, thwarting McKay's and Weir's delaying efforts. Sheppard then storms the gate room and raises the shield, killing all but five of Kolya's reinforcements when they hit the shield.
Kolya contacts Sheppard and lets him know Weir is alive, then threatens to destroy them all and leave if Sheppard doesn't restore power in 10 minutes. Sheppard has no choice but to agree, but before he can he is captured by Kolya's men who aren't in on the plan. Fortunately, Ford and the others arrive and free him. Kolya's aide Sora gets there and then slips away. McKay and Weir get the grounding station going and plan to harness the storm's lightning to power the shield. They return to the control room so Weir can enter the codes to initiate the plan, but McKay tells Kolya he has to evacuate his men since the rest of the base will fill with lethal electrical current.
As they move to regain the control room, Teyla and Beckett run into Sora, who still holds Teyla responsible for her father's death. Sora knocks out Beckett and the two women fight to the death. In the control room, McKay claims he can't get the shield up and Weir convinces Kolya to evacuate. He agrees, but plans to take Weir and McKay with them.
Sheppard and Ford enter the control room, but Kolya uses Weir as a shield – Sheppard shoots around her and Kolya falls backward through the Gate. With time running out before McKay must activate the shield, which will kill everyone outside the control room, Teyla is able to defeat Sora and takes her and Beckett to the control room. McKay activates the shield with seconds to spare. Sora is locked up and after the storm ends everyone offworld returns safe and sound.