The episode stats out with an impending storm hitting Atlantis. The only problem, this storm hit once every 20 years and the ancients before would just plung the city back into the ocean to protect it, but with only 1 ZPM and not enough power to do that, Rodney comes up with an idea of using the lightening from the storm to provide the nessecarly power to raise the shields. The only problem with this plan, the city has to be evacuated for it will cause energy serges throughout the city halls and the genii find out about the plan to evacuate the city and figure it is as good a chance to take what they want from the city as any.
The genii invade the city, outright kill the 2 guards in the gate room, capture Rodney and Elizabeth, and try to find Sheppard. Only Sheppard is finding the genii first and eliminating then as he tries to help Rodney and Elizabeth. Kolya stabs Rodney in the arm, and he cracks under the pain and tells Kolya about their plan to save Atlantis, so Kolya forces Rodney to fix the 3rd grounding station so his plan will work, but Sheppard has disabled the generater to that station. Kolya threatens to kill Dr. Weir and Sheppard runs back to repair the generator, all the while threatening to kill Kolya if he hurts them.
The episode is really a defining moment to show what the people would produce the show can do with a script and special effects. From the background display of the ocean at the grounding stations to the hurricane are amazing for the time.