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.

Anubis's superweapon has been put out of commission, but Yu's fleet has been diverted to the other side of the galaxy by Yu himself, allowing Anubis to escape into hyperspace. Jonas has been captured by Anubis and Daniel is still aboard Anubis's ship, evading capture. Anubis uses the mind probe on Jonas, learns of Naquadria, and begins his attack on Kelowna. The Kelownans seek aid from the SGC. Jack and Sam arrive on Langara to discover that they have given Anubis Naquadria in order to secure their safety. They communicate with Daniel who is attempting to free Jonas. Teal'c has convinced Yu's first prime to seek a new leader of the System Lords, Baal.

A teenage boy shows up at the SGC claiming to be Jack O'Neill. He recalls a dream in which an Asgard was studying him. They determine that they must find this Asgard to fix what has been done to Jack.

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.

On a planet with an extremely toxic atmosphere, there exists a bubble within which exists a livable atmosphere. Inside the bubble lies a seemingly less advanced society of humans. They reveal to SG-1 that they once were highly industrialized and poisoned the air. They voluntarily simplified their lives and constructed the barrier to keep out the bad air. They also show SG-1 their "link", a neural interface that gives them access to all their computer records, including history, science, etc. When one of the citizens disappears in the night and the entire population forgets she existed, SG-1 begins to think things are not what they appear to be.

While investigating a crashed ship, SG-1 finds hundreds of inhabited stasis pods. While doing a thorough count, they are all knocked unconscious by an alien force. When Teal'c wakes Dr. Jackson, Daniel is terrified of him. Upon returning to the SGC, Daniel insists upon getting back to the ship and appears to not know where he is nor who anyone else is.

At a hopeful mining outpost for Naquadah a member of the survey team is kidnapped by an unknown foe. Based on mining artifacts, Daniel speculates that the creature may have been an Unas. When Teal'c finds the missing man as part of a collection of corpses warning others away from the area, their suspicions appear to be confirmed. Daniel brings Chaka to the planet to help negotiate with the leader of the tribe of Unas.

The captain of the Serrakin prisoner transport ship Cerberus seeks Major Carter's help in winning a race and offers in exchange full access to their ion engine technology. He further explains that it is not through official channels and that they will only learn what they pick up by helping him tune up his ship. Sam agrees to help and insists upon running the race with him. However, the competition for this race is steep and there is no telling whether the team will be able to surpass their rivals.

Jay Felger, infamous for his failed projects, and Carter begin work on a computer virus designed to disable a DHD by scrambling its symbols and corresponding coordinates. But when Daniel, O'Neill and the other SG teams become stranded on other planets unable to dial home, Felger's Avenger virus seems to be doing something it wasn't designed to do: it's spreading. As the entire gate network shuts down, Felger and Carter look for a solution to repair the damage that was done.

After being saved by a group of free female Jaffa, SG-1 is taken to the females' homeworld to meet their leader, Ishta. Ishtar proposes an alliance between her all-female rebel group, Haktil, and the Tau'ri. The Tau'ri offer her Tritonin to supplant their practice of taking the symbiotes from defeated Jaffa in the service of the Goa'uld. However, since Tritonin has only had two test subjects, Teal'c and Bra'tac, they are cautious to spread it among their ranks.

Bra'tac and Teal'c encounter a heavily armed enemy with shielding protecting him from Goa'uld weaponry who took out two Goa'uld's personal guards. They barely manage to defeat him and bring him back to SGC for study, but this new threat poses a greater problem for the Tau'ri.

The Tau'ri and Tok'ra have used their captured super-soldier to determine his planet of origin. Though with Daniel, Dr. Lee, and the Ancient device they found in the hands of Honduran kidnappers, SGC must find a way to retrieve them if they are to have any chance of defeating the newly encountered super- soldiers.

During an engine cool down break from hyperspace travel the crew of the Prometheus, with Major Carter as an advisor, encounter a space craft of unknown configuration. They hail the ship to no avail; the unknown craft opens fire upon the Prometheus. Carter attempts to override the safety protocols on the hyperdrive to make a short jump into a gas cloud, but in the attempt is knocked unconscious. She awakes to find the ship devoid of all its crew and, as she tries to escape the gas cloud by herself, she begins to hallucinate.

Jonas Quinn returns to SGC to ask for assistance in saving his nation. He explains that the Naquadriah was originally Naquadah and a Goa'uld started a chain reaction to transform all of his planet's Naquadah into Naquadriah. A large vein of Naquadah has just been affected and the Kelownan scientists believe that the transformation will cause this large a deposit to explode, taking their entire nation with it.

Maj. Carter has been set up with her brother Mark's friend Pete Shanahan, a cop from Denver who thinks Carter works for the Air Force in a simple research capacity. Daniel Jackson is being visited in his dreams by his former lover, Sarah Gardner, who was possessed by the Goa'uld system lord Osiris.

At the new Alpha site, Sam Carter and Selmak (the symbiote carried by Jacob Carter, her father) are working on a new weapon to defeat the Anubis superdrones when the the planet is attacked by a fleet of Goa'uld ships. Carter escapes with the prototype weapon before the base auto-destruct is activated but finds herself being pursued by a superdrone.

The president has asked a documentarian to SGC to create a film about its operations. His arrival is unwelcome to most and he begins to clash with the base personnel. Nevertheless, he conducts his interviews with SG-1 and the scientists in the employ of SGC. Meanwhile, an off-world SG team finds the remains of an Ancient city.

The documentarian still a thorn in their side, SGC encounters an unforeseen predicament. With half of SG-13 off-world engaging enemy Jaffa, SG teams 1, 5, and 7 go in as backup. In the midst of heavy fire, O'Neill takes a staff blast to the chest. Many deaths from the encounter hit SGC hard and Senator Kinsey orders a full investigation into the matter.

Agent Barrett of the NID calls SG-1 to Los Angeles for a consult on a mass murdering of a rogue sleeper cell by a young woman. There they find many Goa'uld artifacts relating to Sekhmet, a subordinate of Ra. But how this operation is related to the Goa'uld eludes SG-1.

The newly inaugurated President of the United States is briefed by the Head of the Joint Chiefs of Staff on the Stargate program. Former Senator, now Vice President, Kinsey attempts to get his running mate to back his policies for the program, but the president decides to look into the situation himself. Kinsey gets Richard Woolsey to convince the president of his agenda.

Vice President Kinsey briefs Dr. Weir on the Stargate program before her meeting with the president. SG teams 1, 3, and 5 go off-world to attempt the extraction of a newly found Ancient repository device. Upon arriving at the location of the device, SG-1 comes under fire from Goa'uld ships. With no other way to disallow Anubis from claiming the knowledge for himself, Jack submits himself to the dangerous device.

With Jack having the knowledge of the Ancient repository once again in his mind, he and Daniel attempt to unearth the location of the lost city of the Ancients. Bra'tac, bringing with him the news of an impending attack on the Tau'ri by Anubis, takes Teal'c to help him acquire ships and warriors for the defense of Earth. Dr. Weir attempts to cope with the overwhelming nature of her new job, while also dealing with the unrelenting ego of Vice President Kinsey.