Flying in a puddle jumper, Maj. John 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 to Atlantis. Dr. Rodney McKay and his colleague Dr. Zelenka determine that the storm is actually two hurricanes merging.
The Ancient databases reveal that every 20 or 30 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 a hidden 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 devise a plan to use electricity from the storm and Atlantis' lighting rods to power the city's forcefield generator and temporarily restore the protective field. But because so much of the city would be electrified in the process, all personnel need to be offworld, except for a handful who would monitor the procedure from the control room.
Meanwhile, Teyla, Lt. Aiden Ford and Dr. Carson Beckett are on the mainland, helping evacuate the Athosians and waiting for the last few to return from a hunting expedition. All but one of the puddle jumpers leave; by the time the hunting party returns, it's too dangerous to fly back to Atlantis. The small group must sit out the storm.
On Manara, the Atlantian relocation is completed. After Smeadon gets an Athosian, Doran, drunk, Kolya and his team come in and force him to dial the stargate code to take them to Atlantis.
Back at Atlantis, Dr. Elizabeth Weir, McKay and Sheppard disable the grounding stations. McKay and Weir are back in the control room, while Sheppard still has one last station to disable. That's when Kolya and his strike team 'gate into the control room, kill the two guards there and take McKay and 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, "Now we'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 descends upon Atlantis....