A test pilot who may have been flying aircraft made with alien technology disappears, and Mulder and Scully must defy their own government to find the truth.
Michael's medical condition forces him to go to the hospital; Lincoln and Sucre get into an explosive situation; Agent Self meets with a shocking ally.
Michael and his crew make their final preparations for the break-in to steal Scylla; Gretchen uses her feminine wiles to obtain the final card key from the general (Leon Russom); T-bag reaches the point of no return.
Michael, Lincoln and Sucre have to crash a police benefit to get the next card key; Sarah falls back into an old habit; on his first day of his new job, T-Bag runs into some old friends and arouses suspicion.
Mahone finds resolution; Gretchen and a Company man get cozy; Michael's medical condition gets worse; a member of the team makes the ultimate sacrifice in the search for Scylla.