Michael and Lincoln are left with no choice but to hand Whistler over in exchange to save LJ and Sofia. A familiar face enters Sona while another inmate leaves.

Clark discovers the reason Lana married Lex then and sets out to kill Lionel. Lex tries to use DNA from the last phantom to power his super-soldiers. Lois goes to a dam to search for Lex's lab but is caught by a security guard and fatally injured. Chloe's power is discovered.

In the season finale, all three couples, Tom and Trina, Roger and Janet and Bruce and Susan, face decisions about their respective marriages as they attend the Deckers's end of summer clambake party.

Butters finds out what his father has been up to late at night and when his mother hears, she overreacts by trying to kill her son and then herself back at home. After returning home and forgiving her husband, she realizes what she has done to her son (she doesn’t know she failed) they spin a story to the media to cover their tracks. Meanwhile, Butters obsesses with returning home so that he can join his parents for an anniversary dinner at Bennigan’s.

Mulder and Scully search for a mysterious man with the power to heal, whose actions risk exposing the existence of aliens on Earth. Meanwhile a confrontation between Mrs. Mulder and the CSM leads Mulder to the discovery of the only weapon which can kill the aliens.