Colonel Jack O'Neill is brought out of retirement to lead a new expedition back to Abydos, only to find an old friend, a new enemy and a far wider use of the Stargate.

The team, now designated SG-1 are planning their next foray through the gate as they try to map out the variety of sites available to them and locate their missing friends. O'Neill asks that Teal'c be allowed to join his team but Gen. Hammond thinks that will be unlikely given that he is the host for a Goa'uld. Unknown to anyone, however, is that O'Neill's close friend, Maj. Charles Kawalsky, leader of SG-2, has been infected by a Goa'uld, an immature version that has not yet taken complete control of the host. Kawalsky is having regular blackouts during which the Goa'uld is trying to return to the gate. An MRI reveals what is wrong but it's unlikely the creature that has fused itself to Kawalsky's spine can be surgically removed. Meanwhile, Col. Kennedy arrives to question Teal'c who has pledged his loyalty to his new world.

The Stargate base is put in deadly peril when it is contaminated with a dangerous infection which causes its victims to become mindlessly animalistic brutes.

SG-1 goes to the planet Cimmeria in search of allies against the Goa'uld. Upon arrival, Jack and Teal'c are trapped in a labyrinth, where the only exit is through Thor's Hammer, a device to destroy Goa'uld, but preserve the host. Daniel Jackson must destroy the device that could someday have saved his wife in order to free his friends.

SG1 travel to a planet where Teal'c is recognised as once having been head Jaffa to Apophis. He is arrested for the murder of a villager and put on trial for his life. Then other Jaffa attack the village. Will SG1 be able to save Teal'c and prove that he has changed allegiance?

On their first visit to a new planet, SG-1 finds it subject to totally destructive volcanic activity and saves ten natives, the Tollan, a far more technologically advanced society. Their leader Omoc isn't grateful, nor interested in such a primitive race as the earthlings or any of the 'even more primitive' planets which are prepared to host them. Only one Tollan, Narim, shows an active interest in life on earth, especially in captain Samantha Carter and the cat Schrodinger she gives him, explaining his planet was destroyed after the Tollan supplied an unlimited energy source to a primitive neighboring planet which abused it for a cataclysmic weapon. Meanwhile, the White House authorized NID colonel Maybourne to take charge over the Tollan for military purposes, exactly Omoc's nightmare.

After arriving on P3X-989, the team are rendered unconscious. When they wake, they return to Earth, but soon find out that they are androids. The team must return to the planet to find out what happened to their real bodies.

While collecting artifacts on a distant planet, Daniel Jackson is knocked out after touching a mirror-like object. He awakens in the same room but is unable to locate the other members of SG-1. Assuming that they left without him, he dials up his return home but gets there to find that he is in a different reality. In this world, General Jack O'Neill and Catherine Langford are in charge of the Stargate program; Hammond is a Colonel reporting to O'Neill; and Sam Carter is a civilian scientist working on the project (and also engaged to O'Neill). More importantly, Earth is under attack from the Goa'uld who have already killed over 1 billion people. Carter believes that somehow, Jackson is from a parallel dimension. When Jackson learns the point of origin of the Goa'uld attack, he wants to return to his own universe, believing that his Earth will be similarly attacked.

Samantha Carter becomes the host of a Goa'uld when she was trying to save the life of the previous host.

SG-1 discovers an ancient artifact and brings it back to the SGC. Ariving at the SGC, it becomes active, pins O'Neill to the gate room wall, and unleashes a virus into him.

The attempt to forge an alliance with the Tok'ra seems a miserable failure, as SG-1 is practically imprisoned as a security risk and considered virtually hostile because 'blending', by agreeing to host a symbiote, is a bridge too far for each of them. When SG-3 arrives and informs Sam about her terminally ill father General Jacob Carter's quickly worsening condition, she realizes the symbiote's healing powers, confirmed to apply to cancer, make hosting an offer to good to refuse for him. Garshaw allows Sam and Jack to return and convince both generals to allow the plan, which is achieved. Meanwhile, the Tok'ra must hastily evacuate, destroying tunnels behind them, because a large-scale attack by Apophis's troops is expected soon, while Jacob meets his potential symbiotic partner Selmak and his equally terminal predecessor to help him decide. Jack verifies his strong suspicion there is traitor among the Tok'ra who is communicating with the Goa'uld.

SG-11 failed to report regularly while mining trinium, a vital mineral for earth's defense against the Goa'uld. SG-1 finds them missing, and all traces cease at the site of arrow-heads made from trinium. Then they are all sedated by such arrows and brought to the village of Tonané, whose earthly tribal ancestry Daniel identifies by its animal totems. However, they are soon awake and released, their guns even returned, and promised to get their friends back, too, from the wolf spirit T'akaya, and the raven-shaped supreme spirit Xe'ls. The council of elders refuses to allow resuming of the mining, which is disrespectful to nature, but Tonané is delegated to be shown alternatives on earth. Both teams return to SGC, or so it appears; in fact, SG-11 is a series of incarnated spirits, who are soon convinced the earthlings are most untrustworthy.

SG-1 travels to a planet whose people are allies of the Asgard.

Daniel falls victim to an invention that swaps his body with that of a dying man.

Colonel O'Neill awakens and is told by new staff everything in the SGC is different because he was just revived after 79 years of cryogenic hibernation, as sole survivor of a disastrous SG-1 mission on a Goa'uld-ruled planet. He accepts to undergo a 'high tech hypnosis' to retrieve information of use in the present war against them, which is going badly, involving earth's ten endangered colonies on other planets. However Major General Trofsky, the new base commander, and his female assistant tell Daniel and Sam, in different sections, that each of them is the sole survivor: it's all make-believe to probe their brains about the weaknesses of earth and the Alliance of the four races. Meanwhile, Teal'c awakes on earth, where it took Dr. Frasier months to save him from death; there was no trace of his teammates, and he resigns when General Hammond refuses permission to keep searching. O'Neill hears Goa'uld language, gets himself free and discovers he's on a fake SGC, frees Sam and Daniel, only to be stopped by the female Goa'uld system-lord Hathor, who employs both Horus and Serpent Jaffa and demands the humans' help against her rival system-lords.

The Asgard and three Goa'uld System Lords meet at Stargate Command to negotiate a treaty modification, but subterfuge and treachery threaten not only the success of the negotiations, but Earth itself.

An alien incursion takes control of the base.

The SG1 team embark on a trip to visit a planet with an idyllic beach, but as soon as they step through the stargate, they find they are back in the SGC. They thought that they just left, but have been missing for hours. They soon discover that an alien device has been implanted in their brains and a being called Urgo reveals himself to the team. But no one else can see him and he is extremely irritating. Will they be able to extract him before they lose their minds?

An old love of Teal'c approaches the SGC and the Tok'ra claiming that her Goa'uld symbiote has been convinced to defect with their help.

When an SG-team member tries to assassinate the Tok'ra leader, it is believed that some of the SGC have been converted into Za'tarc - programmed assassins. The Tok'ra Freya comes to the SGC with Martouf to try and test all SG-team members. But the Za'tarc detector suggests that O'Neill and Carter are actually Za'tarcs. Is this correct and is there another Za'tarc at the SGC?

Col. O'Neill and Teal'c realize they and their friends are trapped in a time loop.

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.

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.

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.

SG-1 finds a Goa'uld-Human hybrid in stasis in an abandoned Goa'uld lab and take it back to Earth to study, where they learn it was created using Anubis' DNA.