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.

A new leader has risen among the Free Jaffa, K'tano, former First Prime of Imhotep. SG-1, accompanied by Bra'tac, seeks an alliance between the Tau'ri and the large force he has amassed.

SG-1 is providing security for three scientists who are conducting research on a far-off planet. Goa'uld warlord Khonsu arranges to capture the SG-1 team and O'Neill tells Jay Felger, nominally the group's leader, to use the gate and head back to SGC. Felger is quite enamored with SG-1, admiring their exploits and daring-do. Rather than follow O'Neill's orders, Felger and another scientist, Simon Coombs, transport themselves up to the Goa'uld ship. What the scientists don't know is that SG-1's capture is a ruse to allow Khonsu, who is actually a Tok'ra, to pass on information. O'Neill is quite annoyed with the two scientists but their presence proves useful in the end.

The Tok'ra are forced to evacuate their newly established base under attack from the Goa'uld. They flee to the SGC's Alpha site. Tensions rise between the allied factions, the Free Jaffa, Tau'ri, and Tok'ra. Jacob and Selmak feel the end of the Tok'ra is near and Sam finds a Naquadah generator has been sabotaged to function as a bomb. Jack suspects the recently arrived Tok'ra and attempts to weed out the traitor.

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.

On a shakedown cruise of the Prometheus, the ship's hyperdrive regulator becomes irreparably damaged. A nearby planet was listed on the cartouche of addresses found on Abydos and thus may have a stargate. After a short jump towards the planet, the Naquadria reactor overloads and must be jettisoned. After the reactor explodes above the planet causing damage, the fate of SG-1 and the crew of the Prometheus is in the hands of a once Goa'uld-controlled world that they're off to a rough start with.

A group of nomads on an alien planet find Daniel Jackson naked in the middle of ruins and take him in. Jonas translates the tablet Daniel said was important and discovers that it describes the last city the Ancients were building before the plague. He surmises that the list of addresses Jack put into the computer while storing the Ancient data were Ancient outposts in temporal order. Thus the last of the addresses should be the "City of the Lost". SG-1 visits the planet and happens upon the nomadic people, now inhabiting the ruins of the Ancient city. There they find Daniel, but discover his memory is gone. They must recover his memories in order to discover the secret to defeating Anubis.

In a firefight with Jaffa, Teal'c takes a staff blast to the gut. Without his symbiote, he cannot regenerate as he once did. Daniel feels that he cannot remember something important, so he goes searching through the logs for any sign of his lost knowledge. Teal'c expresses his feelings that the Tritonin has made him weak.

To save his job, Dr. Felger tests a new virus on the Stargate Network to help control it and it ends up disabling it instead.

SG-1 finds a Goa'uld-Human hybrid in stasis in an abandoned Goa'uld lab and take it back to Earth to study, where they learn it was created using Anubis' DNA.

Vala gambles, wins a cargo ship, but is found cheating; then Adria appears, throws everyone out and claims she has a new Ori fleet and an operational intergalactic Stargate. Vala tells her scary daughter how she helped Daniel, after a dream, reading the mysterious clava thessara-symbol's mystery, which led to a single planet address, where Athena's treasure house must be; after a disastrous visit there, the team refused to follow the next interpretation, fearing it's just a trap set up by Adria, so Vala is declared a security risk, grounded and confined to Area 51, but escapes through the Stargate. Adria takes her along as she hears the team still plans to visit the address, by starship. Upon arrival, they are trapped by SG-1, which however finds itself surrounded by lord Ba'al's troops. Ba'al uses the rings to beam up Adria into an electromagnetic cage in his starship. Back on Earth, General Landry worries what damage the two might do together and wants Adria back. Daniel and Sam now show Vala she has been implanted by Galaran technology with fake recollections of her entire adventure 'til the meeting with Adria. Even though she claims that's impossible, Ba'al is confident he can take control over Adria's loyal Ori troops through her- by implanting a symbiote. The team finds Ba'al's Jaffa and clones killed by symbiote poison, except one Jaffa who secretly used tretonin. The team ring-beams from the cloaked Odyssey starship into Ba'al's, shoots him and captures Adria, but back on Earth, she is found to be under the control of his symbiote. Instead of just killing the evil double, they contact the Tok'ra which send Ta'Seem to extract the symbiote and replace it with a Tok'ra one, but Ba'al manages to poison Adria, who has to be put down. Suddenly Adria wakes up, uses mind-power barricading herself in the sick bay with Vala, tells them she needs time to prepare for ascension, as Daniel guesses outside, and succeeds before the team can cut their way in by blow torch. Nobody knows what this will mean for the future, especially as it remains uncertain whether the Ori are still alive. If not, she may have gained all their former powers, and at least one clone of Ba'al still remains...