The SGC sends a rescue mission to Hathor's base to retrieve SG-1, and O'Neill kills Hathor. Using Tok'ra tunnels already present on the planet, SG-1 escapes and returns home.
The Tok'ra seek a Goa'uld named Seth, who has lived on Earth for thousands of years and now is the leader of a dangerous cult. SG-1 uses zats to overcome the cult members' brainwashing, and in the ensuing rescue, Seth is killed by Carter.
Captain Carter is promoted to the rank of Major. The Asgard warn the SGC that the Goa'uld are planning an attack on Earth. With the help of the Asgard, SG-1 negotiates with three Goa'uld System Lords, Cronus, Nirrti, and Yu, to bring Earth into the Protected Planets Treaty. An attack on Cronus endangers the deal.
On PY3-948, SG-1 finds corpses of several humans who had clearly once had Goa'uld symbiotes. Upon returning, Jackson shows signs of schizophrenia. The cause is a Goa'uld-killer of Ma'chello's (having a strange effect on a non-Goa'uld), and the devices are neutralized.
SG-1 visits a planet named Orban where knowledge is harvested through its children (called "Urrone"). When a Urrone reaches a certain age, their nanites are harvested and they regress to an infantile state and remain that way as the Orbanians have no concept of traditional education.
Using the mirror from "There But For the Grace of God", an alternate Carter and Charles Kawalsky come to the SGC from an Earth that has been invaded by the Goa'uld. SG-1 saves the alternate reality by contacting the Asgard there.
SG-1 is captured by a bounty hunter (Sam J. Jones) who uses them to help catch a Tok'ra named Korra (Mark Holden). The Goa'uld has his race addicted to a drug that can be supplied only by them, but he repents at the last moment and asks Sam to help free his race from the drug.
SG-1 visits a planet ruled by a Goa'uld-infested Unas, who uses the persona of the Devil to keep the residents ruled by fear. They free the people of the 'devil' and instruct them to bury the Stargate.
SG-1 discovers a planet where Apophis was training human slaves to infiltrate the SGC. SG-1 shows them footage of Apophis dying, and they all renounce him as a false god.
After being found on P8X-873, Daniel's wife Sha're is killed by Teal'c to prevent the Goa'uld that controls her from killing Daniel. Daniel quits the SGC and then starts having visions: a residual thought transferred to him by Sha're in the last moments – he must find her son Shifu who is known to be a Harcesis.
SG-1 travels to a world named Vyus (P2Q-463) where the people have lost their memories in an event called the "Vorlix" and are in search of their Elders. The "Vorlix" was following a visit from Linea ("The Destroyer of Worlds", "Prisoners"), and they feel responsible for the problems on Vyus. Ke'ra (Megan Leitch), a young woman with vast knowledge about biochemistry, who assists them to research the world's past, connects strongly with Daniel. Orner is played by Jason Gray-Stanford.
Jacob/Selmak is captured by Sokar. Jolinar was the only person to escape from Sokar's home moon Ne'tu (hell) near the planet Delmak, and Carter has residual memories of the method. SG-1 is captured, and discovers that Apophis controls the moon.
SG-1 manages to escape from Ne'tu with Jacob and Selmak and back to Earth. They use a Tok'ra bomb that blows up the moon and destroys Sokar's ship, killing Sokar with it. Apophis, however, escapes to rise again.
Stargate Command is under control by aliens originating from P3X-118. They use a frequency-based technology that allows them to mimic the appearance of other beings, i.e. humans. Carter must ask Colonel Maybourne to help her retake the base.
Skaara/Klorel crash lands on the Tollans' new homeworld Tollana and the Tollan invite SG-1 to represent Skaara in a trial to decide whether Skaara or Klorel has the right to use Skaara's body. Skaara wins. Lya of the Nox and SG-1 prevent a Goa'uld attack on Tollana.
The members of SG-1 are implanted with an annoyingly extroverted AI named Urgo (Dom DeLuise). They manage to rectify the problem by visiting Urgo's creator on P4X-884, who implants Urgo in himself instead to improve his personality.
SG-1 visits Edora (P5C-768) just in time for a meteor shower caused by the planet passing through an asteroid field. Anticipating significant damage from meteorite impact, they attempt to evacuate the inhabitants. O'Neill is left behind while searching for stragglers. After the meteor shower, O'Neill cannot find the gate, which has been buried by a meteor strike. It takes Carter and Stargate Command 100 days to develop a means to reestablish contact, using a particle beam inspired by Sokar's att
After stealing technology from the Tollan, O'Neill is forced to retire. He joins a rogue SG team dedicated to obtaining advanced technology by any means and then store them on . However, O'Neill was actually on a secret mission as a double agent to find and capture the rogues. He also comes across the Tiernod, a cave-dwelling race on PX3-595 under the protection of the Asgard, who gave them invisibility devices to hide from predators.
SG-1 visits a planet designated P2X-416 where the countries of Bedrosia and Optrica are in the middle of a war about the origin of life. The Bedrosians, who believe a Goa'uld created humans on their world, mistake SG-1 (minus Teal'c) for infiltrators and refuse to accept their account that the Stargate is a transportation device as the Optricans have always claimed. Teal'c frees his team with help from Nyan, one of a minority of Bedrosian scientists willing to approach the Optrican position with
Daniel knows that the Harcesis is on a planet called Kheb; Bra'tac knows how to get there as it is the planet that the Jaffa believe to be the destination of their soul after death (P9C-292). They find a Zen monk who teaches Daniel about the ways of Ascension and an ascended being (Oma Desala) saves the child.
SG-1 finds a Mayan ziggurat in a lepton-rich environment on planet P7X-377; inside is a crystal skull that causes Daniel to be out of phase with our reality. Daniel's grandfather Nicholas Ballard found a similar skull in Belize and helps out. When they return to the planet, giant aliens who have vaguely humanoid but insubstantial forms, appear and return Daniel to normal.
Thor's starship has been infected by Replicators. In order to keep it from landing on Earth, SG-1 disables the deceleration engines so the ship burns up in the atmosphere and crashes in the Pacific. While they attempt escape to P3X-234, one replicator remains.