General Hammond mysteriously retires from the SGC and a new general is brought in, who breaks up SG-1: Daniel and Sam are scientists, Teal'c is with SG-3 and O'Neill commands a new SG-1. O'Neill tries to convince Gen. Hammond to return, but he finds out that someone ordered Hammond to leave or they would hurt his grandchildren. While the others are occupying the new general, O'Neill tries to find out who that "someone" is. Thereto he must place his trust in the one person he hates most: Maybourne.
In 2010, Robert Kinsey is president of a brave new world since he concluded the alliance with the Aschen, a race discovered by SG-1 which lets humanity enjoy its far advanced science and technology, including a vaccine against aging. Sam is now a civilian scientist, married to ambassador Joe Faxon, whose only worry is failing to get pregnant. When she double-checks the Ashen doctor Mollem's computer with Dr. Fraser, who felt superfluous given superior medicine, they discover human fertility is down 90% worldwide in three years. Sam, Daniel and Teal'c turn to retired ...
When a "chosen" boy found on planet Abydos is brought to SGC, he sends a telepathic message, causing Daniel Jackson's personality to undergo disturbing changes. Will the rest of SG-1 be able to solve the mystery of the boy's origin before he becomes a power-hungry warmonger?
SG-5's Lieutenant Barber commits suicide by jumping into the Stargate shortly after a mission on a planet where a since about 200 years abandoned Goa'uld palace is studied by Daniel, who soon develops violent mood swings and is committed to hospital with a neurotransmitter brain condition, presumed fatal after all other SG-5 members die; alas meanwhile SG-3 has visited the planet, finding only the light installation Daniel reported as particularly fascinating and human teenage boy Loran, who hid for Daniel's expedition but now tells Jack he was left there by his ...
On planet Juna, SG-1 minus Daniel gets a hostile welcome from the local warriors leader Darian, who seems incredulous they even dared to return. They loyally deliver Sam and Teal'c, the particularly hated shol'va (Jaffa traitor) to Cronus (who took over as system lord after SG-1 helped chase Heru'ur) and told them to bury the Stargate. Cronus orders Darian to decapitate Daniel by staff weapon- to find his head is robotic. Cronus's obvious astonishment makes Darian doubt his divinity. At SGC, Harlan urge them to go on a mission. The master robot-creator tells them that...
To help Teal'c mind clear again, SG-1 asks Bra'tac to help. Bra'tac removes Teal'c's Gou'ald and Teal'c is forced to remember certain memories of his past. The real Teal'c in the end. SG-1 is glad to have him back.
When Cassandra collapses at home, she is taken to the SGC for treatment. A retrovirus is causing her to emit an EM field and she expresses a need to return to her planet for an initiation ritual. SG-1 investigates and finds a Goa'uld laboratory, probably having belonged to Nirrti, meant for experimentation on the planet's population. They find that the ritual is part of the experiment, a time when Nirrti studies her subjects and cures them when she is done. SG-1 has found a way to cure Cassandra, but now all that remains to be found is Nirrti.
SG-1 teams up with a Russian task force to investigate the disappearance of a Russian SG team on P2X-338. They discover that the Russian SG team released a creature that killed Marduk, a Goa'uld, in his sarcophagus. SG-1 must trust their Russian partners in order to escape the ziggurat alive.
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 Gou-ald, taken from the Russians, and are planning to put it 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 strange ship is headed towards Earth, and the SGC suspects that Martin Lloyd and his companions may have something to do with it. O'Neill is sent to speak to Martin and is assigned as a military consultant on Martin's new show, "Wormhole X-treme!", which uncannily resembles SG-1 despite Martin once again losing his memory. His former shipmates stall Carter and Daniel by throwing them off the trail and into the hands of the NID.