Stargate Atlantis/Recap/S02 E09 Aurora

"You see, the thing is, Colonel Sheppard and I have sort of got into this habit of saving each other’s lives and it’s my turn. (to Ronon) It can be your turn next."

- McKay

The Atlantis long-range sensors pick up a ship coming slowly towards them - an Ancient battle cruiser called the Aurora, reactivated when the city came online. Since it's still about 42 million years away at its current speeds, they take the Daedalus to go check it out.

They discover that the entire Ancient crew - more than 400 strong - are still alive in the same sort of stasis pods that Weir used to return to Atlantis. After ten thousand years, the people are too old to be revived without killing them, but they are nevertheless showing considerable mental activity in some kind of massive network. While Ronon and Teyla explore the ship, McKay plugs Sheppard into a spare pod to interface with the network and see what he can learn.

He finds himself in a virtual reality world, where the Captain and crew of the Aurora are trying desperately to repair their hyperdrive, in order to return to Atlantis with all possible haste. They have discovered the Wraith's secret weakness, recorded in a communique, which they hope will alter the course of the war. Sheppard tells them that the war has been over for ten thousand years and that nothing around them is real, but the information in the communique would still be absurdly useful to their distant descendants. Naturally, they respond by throwing him in the Brig.

Meanwhile, the Daedalus sensors have detected two incoming Wraith cruisers. Caldwell radios in and tells the team they have 20 minutes to get out before he has to a) destroy the ship to prevent the Wraith from getting their hands on it and b) disappear into hyperspace to prevent the Wraith from learning that Atlantis wasn't destroyed. They pointedly refuse to tell him that Sheppard has gotten himself be-stasised. What's worse, they discover that one of the people in the virtual network, the hot but obstructive first mate has been replaced by a Wraith infiltrator. McKay decides it is his duty to go in and rescue Sheppard, or at least see what's taking him so long.

Whereupon he, too, gets immediately captured and thrown in the Brig. By comparing notes with Sheppard, they surmise that the Wraith is keeping the captain focused on the hyperdrive rather than the communique in order to gain access to the Ancients' intergalactic (rather than interstellar) drive technology, and thus reach the Milky Way Galaxy and Earth. McKay pops back out of the system and uses some complex jiggery pokery to turn off the guards and the door, and the two of them go to take down the Wraith and convince the captain of their case. The amazing disappearing reappearing Sheppard trick does wonders on the Captain's credulity, and McKay is able to throw the Wraith out of the system. Unfortunately, the Wraith has long since erased the communique (and by now nobody remembers what was actually in it) - and McKay now has a conscious and very angry Wraith on his hands.

Sheppard pops back out of the system after a serious talk with the Captain, shoots the Wraith, and radios a justifiably irate Caldwell to beam them all out of there. Caldwell is annoyed because the two Wraith cruisers have arrived, and he's unsure how he's going to both destroy the Aurora and prevent the Wraith from telling anybody about them. Sheppard explains that the Captain gave him the Aurora's self-destruct codes. As the Wraith cruisers converge on the Aurora, the Daedalus hurries to a safe distance and the Ancient ship explodes, taking the Wraith with it.

Tropes

 * Ancient Popsicles
 * Ghost Ship
 * Inside a Computer System
 * It Has Been an Honor: the Captain's final speech to his crew before blowing up the Aurora
 * Smart People Play Chess: In the beginning of the episode, Ronon and Weir watch two scientists...think about chess. Ronon is not impressed.