Remnants

John Sheppard has been abducted. After freeing himself from his bonds, he soon discovers who it is who tied him up: Acastus Kolya (Robert Davi). In Atlantis, Woolsey, McKay, and the rest of the team are about to make a shocking discovery about an ancient race called Sakari, a silicon-based lifeform, which uses severe hallucinations into manipulating them into doing the right thing when a Sakari seed carrier is found in the ocean. Xiao Shen, an IOA dignitary, comes aboard to judge Woolsey's ability to be a capable commander and is planning on using this situation so she can get control of Atlantis herself. Eventually its revealed that both Kolya and a woman Woolsey was attracted to are projections of the Sakkari AI trying to distract Sheppard and evaluate Woolsey. The AI wants Woolsey's help to save its race from extinction by transporting it to its target world after it had crashed on Atlantis' home world thousands of years ago. It was trying to distract Sheppard as he was the greatest threat to it, but it never meant him any harm. Woolsey decides to help it even though it could cost him his job and has the Apollo transport it where it needs to go. As a final thanks, the AI tricks the dignitary and saves Woolsey's job.