A teenager claiming to be ColonelJack O'Neill arrives in Stargate Command. Believing him to be an imposter, the teen manages to recite every key event from fellow team members. After believing it to be O'Neill, they find out he's a botched clone. They investigate what has happened to the real O'Neill.
Teal'c is shot on a mission and is determined to make his recovery as quick as possible, since Rya'c and Bra'tac have been captured and work as slaves on Erebus. Dr.Daniel Jackson starts to remember a few events from his time while he ascended, and uses them to aid several SG teams to infiltrate the labor camp and rescue the imprisoned Jaffa.
SG-1 finds a civilization living in a Dome on an unlivable planet. The seemingly peaceful civilization use geothermal energy to maintain the dome. However, mysteriously, several people start disappearing, and the dome is slowly shrinking.
While examining a crashed alien ship called the Stromos, Dr.Daniel Jackson is struck with a power surge. After returning to Stargate Command, it is discovered that several consciousnesses from the people trapped in stasis are in Jackson's head.
SG-1 encounter the Hak'tyl Resistance, a group of rebel Jaffa females who renounced their "god" Moloc as a false one, after realizing he had ordered all young females to be put to death. SG-1 propose that they no longer need to rely on symbiotes, since they are running low on them, and offers them a substitute, Tretonin. Meanwhile, Teal'c gets closer to the Hak'tyl leader, Ishta.
Anubis has created an army of invulnerable killing machines called Kull warriors to do his work and wipe out the rival Goa'uld. They have armor that impervious to all known weapons. The only way to stop them is for Dr.Daniel Jackson to go to a hidden temple in Honduras that is the origin of the "fountain of youth" myth.
Dr.Daniel Jackson and Dr.Bill Lee are captured by Honduran rebels after getting their hands on a device that could stop the Kull warriors. As ColonelJack O'Neill launches a secret mission with an old acquaintance to retrieve the two, the rest of the team uncover more information on the warriors by infiltrating Tartarus, the planet on which they are created.
While on a routine journey to Earth, the Prometheus makes first contact with an unfriendly ship, and is attacked. Whilst retreating to a Interstellar cloud, MajorSamantha Carter is knocked unconscious. She awakens only to find the ship completely abandoned in the Interstellar cloud, but has several hallucinations of the rest of team, and a little girl named Grace.
SG-1 minus ColonelJack O'Neill are in Los Angeles where the NID discover a rogue experiment. Also, a Goa'uld explosive device is activated, and they have only hours to deactivate it, or the entire city will be destroyed.
Anubis is sending his entire fleet to Earth to gather the whereabouts of the Lost City. Meanwhile, ColonelJack O'Neill, who is starting to get affected by the Ancient knowledge, leads SG-1 to Proclarush, which is believed to be the location of the Lost City, only to find that they have to return to Earth, which is the location of the city, Atlantis.