Woolsey admits to Teyla, Ronan and Dr. McKay that he's apprehensive about an upcoming performance evaluation. Later, while en route to his quarters, he encounters Dr. Vanessa Conrad, an engaging scientist recently arrived on the Apollo, and finds himself more than a little attracted to her. But she is quickly forgotten when I.O.A. representative Shen Xiaoyi appears and advises him that he's been reassigned to a new position back on Earth. Woolsey is shocked by this news but, aided by his new acquaintance, elects to fight the I.O.A.'s decision.
Col. John Sheppard, meanwhile, has flown several astrobiologists over to the mainland for a two-day research expedition. On his way back to camp, he is ambushed and captured by an old foe hell-bent on acquiring Sheppard's identification code.
Back on Atlantis, McKay and Zelenka investigate a mysterious object discovered at the ocean's bottom.