As the storm approaches, Commander Kolya of the Genii, who has seized Atlantis, is about to shoot Dr. Weir. Suddenly, Dr. Rodney McKay steps in front of the gun and convinces Kolya that he and Weir are the only ones who can fix Grounding Station 3 - the last of the four grounding stations that must be disabled so that lightning from the storm can be channeled into the shield generator, to power up the shield and protect Atlantis from being obliterated. Kolya spares their lives, but contacts Maj. John Sheppard over the radio and tells him that Weir is dead. Sheppard vows to kill Kolya.
Meanwhile, on the mainland, Lt. Aiden Ford, Teyla and Dr. Carson Beckett are waiting out the storm in a puddle jumper. Suddenly, the wind stops and the sky clears. They are in the eye of the storm. Ford commands a reluctant and frightened Beckett to fly the Puddle Jumper straight up the eye, over the storm to Atlantis to help Sheppard.
On Atlantis, a female Genii named Sora reports to Kolya that Sheppard has killed three more of their men. Weir and McKay, who are working to bypass the broken switch on the grounding station, overhear the conversation and try to stall the repair to give Sheppard more time. Kolya commands Sora to radio Chief Cowen, leader of the Genii, to send a full company of 60 men through the stargate, dashing Weir and McKay's hopes of rescue.
Sheppard disables the generators powering stargate operations and Grounding Station 3, making it impossible for McKay and Weir to finish their task. Sheppard then storms the control room and raises the 'gate shield. Only five of Kolya's 60 men get through. The rest are destroyed by the shield.
The storm is less than an hour away.
Kolya radios Sheppard with a proposition. If Sheppard doesn't restore power to Grounding Station 3 in the next 10 minutes, Weir really will be killed, followed by McKay 10 minutes later. Sheppard, relieved to hear Weir's voice, has no choice. Joined by Ford, Teyla and Beckett, he restores power to Grounding Station 3. McKay disables the station.
In the control room, Kolya orders McKay to power up the shield. McKay and Weir bluff Kolya into believing that McKay's plan has failed and that Atlantis is lost. He decides to withdraw, but also to take Weir and McKay with him. Sheppard and Ford storm the control room and kill Kolya's remaining men. Kolya uses Weir as a human shield and backs toward the activated stargate. Sheppard takes the shot and hits Kolya, who releases Weir as he falls backward through the 'gate.
With the storm due to hit in 2.5 minutes, Teyla and Beckett are unaccounted for. That's because Sora has knocked Beckett unconscious and is fighting Teyla, whom she believes to be responsible for her father's death. Teyla wins but lets Sora live. Sora follows Teyla, who drags Beckett to the control room. Weir gives McKay the order. Lightning strikes Atlantis and floods the corridors. The shield activates just before a huge wave hits the city.
Atlantis is saved and Weir orders Sora held as a prisoner.