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When Atlantis made first contact with the Genii, they appeared to be a community of simple farmers. However, it was quickly discovered that the Genii had secretly developed relatively advanced technology to combat the Wraith. This led to an alliance between the two groups. The Genii were impressed by Tau'ri technology, namely their C-4 explosive, which could be used to perfect their atomic bombs.
Working with the Genii, the expedition mounted a raid on a Wraith Hive ship to steal intel on the location of their fleet. The Genii Tyrus was captured by the Wraith, and the Genii blamed his loss on the expedition. They attempted to take their supplies of C-4, as well as their Puddle Jumper. Having expected such an outcome, Major John Sheppard turned the tables by having two Jumpers lie in wait. Sheppard took the Wraith data storage device from the Genii as compensation, leaving both parties at odds. (SGA: "Underground")
Upon discovering a massive storm heading towards Atlantis, Dr. Rodney McKay wasn't sure the city would manage to survive it without the shield or submersion capabilities. Therefore, Dr. Elizabeth Weir decided to evacuate all expedition members, except several key personnel, while McKay and Dr. Radek Zelenka attempted to use lightning as power source for the shield. This information was leaked by the Manarian Smeadon to Cowen of the Genii, who saw it as a perfect opportunity to raid the city. He assigned Commander Acastus Kolya to lead a strike team to Atlantis, over objections that they were not prepared for it. (SGA: "The Storm")
Using an IDC acquired from the Athosian Doran, and posing as wounded Athosians, Commander Acastus Kolya's strikeforce was granted access to Atlantis. He immediately killed the two guards who attempted to help, despite earlier claims that they would be subdued non-lethally, and took control of Stargate Operations, where Dr. Elizabeth Weir and Dr. Rodney McKay were waiting for Major John Sheppard. Sheppard, meanwhile, was on the far end of the city, operating a grounding station. Teyla Emmagan, Lt. Aiden Ford and Dr. Carson Beckett were trapped on the mainland, unable to liftoff due to the storm.
Kolya demanded the Wraith data storage device Sheppard had stolen from them, as well as their entire supply of medicine and C-4; McKay managed to broadcast his demands to Sheppard, who then hid the C-4 before it could be taken. Sheppard offered to give it to Kolya in exchange for the release of the hostages, assuring him that they would be allowed to leave Atlantis unharmed. However, Kolya had already learned of the plan to save Atlantis from McKay, and now intended to seize the entire city for the Genii.
At Kolya's insistence, Sheppard continued to the final grounding station so the lightning from the storm could power the city. The Genii attempted to ambush him, and though Sheppard came out of the skirmish victorious, the controls to the station were damaged, making it impossible to disable. In retaliation for the deaths of his men, Kolya decided to execute Weir, ignoring Sheppard's pleas.
McKay convinced Kolya that Weir was vital to the success of the plan, so Kolya spared her, though he claimed otherwise to Sheppard who monitors the Genii's movements through a stolen radio. Koyla brought McKay and Weir to the grounding station to repair it while his men attempted to kill Sheppard guided by Ladon Radim through the city's sensors. Using a life signs detector and his superior knowledge of the city, Sheppard systematically killed Kolya's men while sabotaging the Naquadah generators powering the city, including the one powering the Control Tower and the remaining grounding station. Kolya attempted to call for reinforcements to bolster his dwindling forces, but Sheppard infiltrated Stargate Operations and activated the Stargate shield, killing all but five of the sixty soldiers that were sent through. At the same time, Sheppard also killed one of Koyla's men while shooting blind escaping from the Control Room.
Beckett's Jumper finally was able to liftoff in the eye of the storm, so they set course for Atlantis to help Sheppard. Meanwhile, Kolya, tired of Sheppard's resistance, told him that Weir was alive, but warned that he would kill both her and McKay if it became clear the city could not be saved. Sheppard was thus forced to restore power. Ford led Teyla and Beckett to help Sheppard, unaware of his predicament. The Genii managed to ambush Sheppard at the necessary generator, but Ford's group arrived in time to rescue him, stunning the two who presumably died in the lightning strikes later. McKay was finally able to repair the damaged grounding station after power was restored. With Atlantis no longer grounded, everyone was required to fall back to the control room, as the corridors would be charged with electricity in the rest of the city.
Sora Tyrus, who happened to be nearby when Sheppard was rescued, spotted Teyla and broke ranks to hunt her down. Sheppard directed Teyla and Beckett to the Jumper bay, intending to have them lower a Jumper into the gate room as a distraction. Sora ambushed Teyla here, knocking Beckett unconscious and challenging Teyla to a knife fight. Teyla was victorious, but refused to kill Sora who seemed to finally give up on her mission of vengeance afterwards. (SGA: "The Storm", "The Eye")
Dr. Rodney McKay pretended to be unable to activate the city's shield and Dr. Elizabeth Weir convinced Commander Acastus Kolya to evacuate before the full force of the storm hit. With no shields and a tsunami coming, Koyla ultimately saw no choice. However, Kolya decided to bring McKay and Weir with him as punishment for their crimes against the Genii. With Teyla Emmagan indisposed, Major John Sheppard and Lt. Aiden Ford were forced to take action. They managed to take out most of the remaining Genii forces with the only survivors being the few that got through the Stargate before they started shooting and Ladon Radim who dove through as they fired. Kolya attempted to use Weir as a human shield, but Sheppard's superior aim allowed him to shoot Kolya in the shoulder without harming Weir, causing him to fall backwards into the event horizon alone.
Aided by Sora Tyrus, Teyla brought Dr. Carson Beckett to the control room. McKay activated the shield using the power from the lightning, saving the city from destruction by the approaching tsunami. (SGA: "The Eye")
The city survived the storm intact, though several areas were flooded, and the evacuated members of the expedition returned home. Sora Tyrus, having been left behind during the Genii escape, was locked in a cell temporarily, though Weir intended to return her to the Genii as an act of good faith. Commander Acastus Kolya survived the gunshot wound and considered Major John Sheppard his sworn enemy. (SGA: "The Eye", "The Brotherhood")