Members of SG-1 become infected with an alien virus that turns them into primitive beings. Dr. Fraiser must find a cure to save the team and the alien population from whom it was contracted.

SG-1 locates the Tok'ra, a Goa'uld resistance movement who oppose the System Lords, and attempt to form an alliance. Jacob Carter's cancer brings him near death.

While SG-1 tries to form an alliance with the Tok'ra, a spy betrays the rebels to the Goa'uld. Jacob Carter finds that the Tok'ra may be his only hope of survival

O'Neill, Carter and Jackson must escape Hathor's clutches, while Teal'c tries to raise a Jaffa army on Chulak. General Hammond must take desperate measures to rescue the team.

O'Neill steals technology from the Tollan, and is forced to leave the Stargate program. Maybourne offers an intriguing proposal.