Asuran invasion of Atlantis

History
After the Ancients retook Atlantis from the expedition, the Asurans made another attempt to take Atlantis, by sending one of their ships there. The Ancients believed that the Asurans couldn't harm them due to a directive in their base code which prohibited it, but due to Dr. Rodney McKay's tampering with the base code, they were able to erase it and attack the city, which they destroyed much of. The Ancients were all killed and the only survivors were Richard Woolsey and Major General Jack O'Neill who were there negotiating with the Ancients at the time and managed to hide out in damaged areas of the city where the sensors weren't working. Due to standing orders from O'Neill, Major General Henry Landry dispatched the Daedalus to nuke the city, but Lt. Colonel John Sheppard, McKay, Dr. Elizabeth Weir and Dr. Carson Beckett launched a daring attack to retake the city, recruiting Teyla Emmagan and Ronon Dex to help as well.

Upon arrival they dropped a bomb that damaged the Control Room and main tower and took the Jumper to space to pick up the frozen Niam, in order to use him as part of their plan to freeze the Asurans, so they could kill them all with the newly acquired Anti-Replicator gun. Upon return to the planet, the Asurans launched Drone weapons after them, which they lost by diving into the water and entering an underwater Jumper bay. The bay was flooded, the automatic pumps weren't working, the outside doors wouldn't open, and the Jumper also had water leaking into it through a crack, so the team had O'Neill use a dead-man's switch to activate the pumps and drain the water. Unfortunately, O'Neill and Woolsey were captured, their minds were probed, and the Asurans learned of the plan, so they reactivated Niam to stop them. McKay managed to kill him with an ARG, but it ruins their plan. They come up with another plan where they plant the ARGs crystals in the shield emitters causing the shield to emit an Anti-Replicator field, when activated and also plant C-4 to throw off the Asurans if they are captured.

As part of the plan, they let Woolsey and O'Neill know that they plan to blow the emitters so when the Daedalus arrives, it can nuke the city, knowing their minds will be probed which would let the Asurans in on the false plan, tricking them. O'Neill knew they were lying, since he noticed Lt. Colonel Samantha Carter do similar plans, and Woolsey bought the false story completely. The Asurans fire up Atlantis' Stardrive, but as they haven't finished planting the crystals, Beckett disables it with a few drones (although the Asurans ultimately fixed the damage done) and they all get captured, but everything goes according to plan as the Asurans activate the shield when they detect the Daedalus and are destroyed. The team contacts the Daedalus and convinces them of the Asurans destruction, having the crew send down a team of Marines to verify their story. Since the Ancients were all killed, O'Neill lets Weir and her expedition stay.