Carter gets kidnapped and taken to an abandoned hospital where two doctors work to study the remains of Jolinar. She finds out that they have a Goa'uld, taken from the Russians, which they are planning to put inside a man named Adrian Conrad to heal his sickness. They need Carter to tell them how to get the Goa'uld out after he's healed. O'Neill believes the government is involved with Carter's disappearance and contacts Maybourne. Together, with Daniel and Teal'c, they find Carter but also find out that the Goa'uld has escaped inside Conrad's body.

The Russian SG team brings back a man who claims that his people are being experimented on by Nirrti. SG-1 investigate where the experiments are conducted, with the Russian SG team as backup. The inhabitants worship Nirrti as their god and savior from a terrible plague. SG-1 attempts to use the same device Nirrti used on the people to reverse the mutations, but the people turn on them at the arrival of Nirrti.

The discovery of the Stargate creates a war between two nations on the planet Tegalus with Daniel in the middle of it.

Ex-Vice President Kinsey comes to Jack informing him of the Trust's activities including what seems to be a plan for the Russians to reclaim the Stargate they lent to the United States. He decides to use Kinsey as their inside man with the Trust. Kinsey wears a wire for his meeting with the Trust to set up a meeting with a high-ranking Russian general. The plan goes south when the signals get jammed just as the Trust makes an astounding revelation to Kinsey and they beam out.

Based on the information Vala gave them, SG-1 travels to the planet where Merlin may have hidden his secret weapon to defeat ascended beings. There they find an appropriately medieval village and learn that Merlin kept a library there. The locals have never been inside owing to a curse on anyone who dares enter, but SG-1 finds a way in. Once inside, they find a secret chamber that may reveal the location of the weapon. The SGC, meanwhile, has located the Ori's Supergate. Sam's attempt to get control of it is too late, and four Ori ships make their way through. In the ensuing battle, much of Earth's fleet is destroyed, and the future of several SGC members is left in doubt.