The SG-1 crew finds an amnesiac Daniel Jackson while visiting a planet in its search for the City of the Lost. After bringing him back to SGC, they begin to formulate a plan to destroy Anubis' power core and lure Anubis into their midst. Soon Teal'c is taken prisoner by Lord Yu after Yu backs out of a deal to help SG-1, while Anubis captures Jonas to get info on his home planet, Kelowna.
Jonas' home planet, Kelowna, asks SGC for help against an attack from Anubis, as he pursues a Stargate on Kelowna's main base. The Kelownans then combine forces with their enemies, Andari and Tyrania, to combat Anubis.
A young O'Neill shows up and claims he's the real Jack O'Neill with no memory of how he came to deage except for possibly an experiment that was performed on him during an abduction by the Asgard. After verifying the DNA is that of O'Neill, the SG-1 crew come to learn that young O'Neill is actually a clone.
Teal'c is wounded as SG-1 returns to the SGC, but becomes discouraged by the slow recovery caused by the absence of his symbiote. Meanwhile, Daniel begins to remember a prison planet where he saw Rya'c, prompting SG-1 to launch an attack on the planet known as Erebus, where Teal'c then attempts to rescue his son.
SG-1 discovers a planet where the people live in an idyllic oasis under a computer-controlled force field dome.
The SG-1 team discovers hundreds of people on a spaceship, suspended, motionless, in chambers that give off a glowing energy. All the members are knocked unconscious by the energy force, but when Daniel awakes, he begins to exhibit the personality traits of several of the ship's inhabitants.
While looking for a mine on the planet Naquadah, the SG-1 discover the presence of Unas on the planet when one of their crew members is killed, prompting Daniel to attempt a truce negotiation.
Carter volunteers to help Warrick the pilot win a race and agrees to supply him with a generator in exchange for the chance to study the Hebridan's advanced technology. While Teal'c and Eamon are captured while guarding the ship, Carter and Warrick must save another pilot and discover the kidnappings are all part of a plot by humans to sabotage the race.
A newly-invented virus designed to target enemy Stargates is used by its scientist creator against the Goa'uld and Ba'al, a move which, instead, downs the whole Stargate network.
During a meeting between SG-1 and a group of Jaffa, SG-1 are captured by female Jaffa rebelling against the system lord that kills the women, and taken to their planet's base. During that time, Teal'c forms a bond with Ishar, the rebel Jaffa's high priestess.
Daniel is captured in Central America, prompting O'Neill to mount a rescue effort. Meanwhile, Carter and Teal'c face a growing menace, an unstoppable form of Goa'uld supersoldier brought on by Anubis.
Daniel travels to South America in search of a device whose owner was rumored to be a system lord known as Telchak. When Daniel is suddenly captured, O'Neill is sent to retrieve him, while Carter and Teal'c research a powerful enemy, dealt by Anubis, which plans on destroying the system lords.
Carter finds herself stranded on the ship Prometheus while on a retrieval mission, during which time she has a series of eerie and frightening visions.
The SG-1 crew returns to Kelowna when it learns that Jonas is digging beneath the surface to prevent the destruction of the planet from a massive explosion at the its core.
Carter's new relationship with a police officer becomes complicated, and potentially dangerous, when he suspects she's hiding things about her work and begins to investigate her. Meanwhile, Daniel is troubled when Osiris begins manipulating the content of his dreams.
The Goa'uld pinpoints the location of the Alpha Site, and Anubis' forces attack. As the site is evacuated, Teal'c and O'Neill try to find Carter, who is fighting for her life somewhere on the site. Meanwhile, the allies suspect there is a spy in their midst.
A film crew is sent by the President to shoot a documentary on standard operating procedure at the SGC, but the crew sees more than they were expecting when the Stargate team gets caught up in a grave interplanetary mission.
Bregman continues to grab video footage wherever possible for his television project, tagging along with the SG-1 crew as it continues to grapple with an off-world mission gone awry. Unfortunately, an attempt to save another crew member during the mission costs Dr. Fraiser her life.
Carter and Daniel learn that the NID has been experimenting with genetic research and discover its creation, the human-Goa'uld Anna, who can use the ability to reproduce the images from her dreams to disarm the bomb embedded inside her with which she has held her creator captive.
Newly in office, Vice President Kinsey tries to coral the SGC and get an order from the president which would put it directly under his authority.
The SG-1 team prepares itself to avert Earth's complete destruction at the hands of Anubis' as it seeks the solution within the Lost City of the Ancients.
As the SG-1 team continues operate on the belief that the Lost City of the Ancients will hold the information needed to keep Anubis from destroying Earth, O'Neill begins delving into that information, which was implanted into his mind by the Ancients. The team also comes across what they believe to be the long lost city of Atlantis.