While Vaughn's life hangs in the balance, Lauren butts heads with Sydney after learning the part she played in his stabbing. Meanwhile, Sydney further questions Sloane's allegiances after he is kidnapped by Kazari Bomani, a kingpin in The Covenant; Jack's cover is jeopardized when he meets with Simon to dig up information on Sydney's missing two years; and Marshall is sent on his second mission with Sydney, posing as a high-stakes, southern gambler.

Sydney and Vaughn must track Kazari Bomani down to get hold of a piece of the Rambaldi puzzle. Meanwhile, Jack reveals his suspicions to Senator Reed about his daughter Lauren's allegiances, and Vaughn decides what to do about his marriage.

Sydney and Jack warn a disbelieving Vaughn about their suspicions of Lauren being the CIA mole. Meanwhile, Bomani and Sark take possession of the Rambaldi machine, Sydney and Vaughn must stop a Covenant virus that's crippling medical facilities around the world, Sloane's secret is revealed to Jack, and Bomani begins to lose faith in Lauren's ability to carry out her Covenant missions.