Flying in a Puddle Jumper, Sheppard and Teyla witness a gigantic storm front covering 20 percent of the planet. It's tracking toward the Athosians' mainland settlement - and then straight toward Atlantis. Dr. McKay and his colleague Dr. Zelenka determine that the storm is actually two hurricanes merging.
The Ancient databases reveal that every twenty or thirty years the Atlantian ocean gets unseasonably warm, creating weather conditions conducive to such perfect storms. In the past, Atlantis was either underwater or else its force field protected it. But now, without the field, the only answer is to ask another planet's race to put them up until the monster hurricane blows over.
Smeadon, leader of the Manarians, complies with Sheppard's request on the condition that the Atlantians will owe him a favor. But Smeadon has yet another agenda: He puts in a call to Cowen, leader of the Genii, of whom Atlantis has made an enemy. Cowen has his finest military officer, Commander Acastus Kolya, assemble a strike team that heads to Manara.
Back at Atlantis, McKay and Zelenka come up with a plan to use the electricity of the storm and Atlantis' lighting rods in order to power the city's force-field generator and so temporarily raise the protective field. But because so much of the city would be electrified in the process, all personnel would have to be offworld except for a few who would monitor the procedure from the control room.
Meanwhile, Teyla, Lt. Ford and Dr. Beckett are on the mainland helping evacuating the Athosians and waiting for last few to return from a hunting expedition. All but one of the Jumpers leave, and by the time the hunting party returns, it's too dangerous to fly back to Atlantis. The small group must sit the storm out.
On Manara, the Atlantian relocation is completed. Then after Smeadon gets an Athosian, Doran, drunk, Kolya and his team come in and force him to take them to Atlantis.
Meanwhile Weir, McKay and Sheppard go about disabling the grounding stations in Atlantis. McKay and Weir return to the control room after completing their tasks, while Sheppard still has one more station to disable. That's when Kolya and his strike team gate into the control room, kill the two guards there and take Dr. McKay and Dr. Weir hostage. Sheppard tries to deal with Kolya over the radio, but the invader isn't listening.
He sends men to kill Sheppard, but Sheppard kills them instead. Sheppard tells Kolya over the radio that now they're even. But Kolya doesn't see it that way. He is about to shoot and kill Dr. Weir. Sheppard screams into the radio that he'll do whatever Kolya wants. But Kolya has switched off the radio. He is about to pull the trigger. Outside, the storm is about to hit Atlantis....
(to be continued)