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.

As the Goa'uld attack fleet approaches Earth, all four members of the SG-1 team are taken prisoner. They get help from an unexpected source when Bra'tac, Teal'c's mentor, reveals that he is on board. Apophis has delayed the attack until his son Klorel is revived, giving them some time to prepare. SG-1 has used all of the C4 on one of the two ships but must find a way to dispose of the second. Back at Stargate Command, Lt. Col. Bert Samuels arrives as a Pentagon liaison officer but also reveals a new weapon they have developed. General Hammond is dubious. They begin to transport humans to an Alpha site in order to ensure the continuation of mankind.

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

SG-1 inadvertently help a desperate criminal and are charged and sentenced as accessories to his crime. They are banished to a desolate, brutal penal colony and strike a deal with a powerful female prisoner to help them escape. But is this prisoner hiding something from them?

Exploring a strange and beautiful garden, SG-1 comes across a dome containing a race that are connected to machines. The team are captured by the machines and rendered unconscious, but awake to find themselves reliving pivotal moments of their lives, over and over again. Then they discover it is virtual reality and a mysterious keeper appears to persuade them to try different outcomes for the moments. But can the team escape his clutches, when they don't know what is real and what is not?

O'Neill and the team return to Cimmeria, the planet where they destroyed Thor's Hammer to help Teal'c escape. They find that the Goa'uld have invaded and many of the people are dead. Can they help to find Thor's weapons to fight off the invasion before they are all captured or killed?

Teal'c's son Rya'c is kidnapped by Apophis and SG1 tries to rescue him. When Rya'c is recovered he denounces his father and helps to capture the team. They escape, but will they be able to return to Earth and cure Rya'c?

While exploring a new planet, Teal'c is stung by a giant insect whose venom causes a terrifying transformation.

When Teal'c makes Sam Carter realize how valuable the knowledge left by Tok'ra Jolinar in her brain and the chance for an alliance can be, they convince General Hammond to let SG-1 attempt a meeting. They arrive on a planet which is deserted on the surface, but are awaited by well-camouflaged, armed Tok'ra who bring them to tunnels which they create by means of a mysterious crystal, which can also undo them afterward. Both parties are quite suspicious, the team feels like captives, and indeed, the Tok'ra leader Yosuuf fears they cannot be released, at least until the whole site is moved. Meanwhile, the Tau'ri barely overcome their suspicion against the Tok'ra Goa'uld biology (with symbiote), when asked to volunteer themselves as 'hosts', and Carter learns Martouf (and his symbiote, Lantash) was Jolinar's lover, hence has a special connection with her.

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.

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.

While employing the help of a planet's highly intelligent children for a project, the team discovers their horrific imposed fate when they reach a certain age.

The SGC is visited by a Tok'ra named Anise who brings some armbands used by the soldiers of a long extinct race, which are supposed to increase the abilities of the wearers. O'Neill, Carter and Jackson put the armbands on and it increases their physical strength, but it also causes them to make rash decisions. Can they get the armbands off before they cause their deaths?

The newly inaugurated President of the United States is briefed by the Head of the Joint Chiefs of Staff on the Stargate program. Former Senator, now Vice President, Kinsey attempts to get his running mate to back his policies for the program, but the president decides to look into the situation himself. Kinsey gets Richard Woolsey to convince the president of his agenda.