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.

General Hammond has tried everything to get the Senate's decision to shut down his Stargate program undone, but the President personally refuses to 'commit political suicide': the Stargate will be buried. Daniel's insistence -that the danger for Earth as a whole outweighs everything- convinces his colleagues to ignore Hammond's command and dial the address that the Goa'uld invasion started from in the alternate reality that he visited. They arrive not on a planet but a new, superior type of starship, already launched by hyper-drive. A 'video' proves it belongs to Apophis, who gives command to his son Klorel, whose host is none other than the team's young Abydonian friend, Skaara. Overpowering Skaara seems their best move, while Sam installs explosives in the death glider deck with a 24-hour timer just in case, but the Jaffa manage to liberate Klorel. Jack discovers that the ship goes far faster than expected.

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.

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 SG-1 team is requested by the Tollan to participate in a trial concerning Skaara and whether he or the Goa'uld parasite, Klorel, has control of his body.

To help Teal'c's mind clear again, SG-1 asks Bra'tac to help. Bra'tac removes Teal'c's Goa'uld and Teal'c is forced to remember certain memories of his past in order to get back to the real Teal'c in the end. SG-1 is glad to have him back.

Riding in the elevator in the SGC, O'Neill is visited by Daniel Jackson who needs his help. Daniel tells him that Anubis is headed for Abydos to search for something called the Eye of Ra, a relic that would make Anubis all-powerful. It's essential that SG-1 go to Abydos and secure the Eye but no has seen it - including Daniel - nor has anyone ever been able to find it. On the planet they see their old friend Skaara and with Daniel's help locate the Eye. They also find a tablet that speaks of a lost city of the ancients. When Anubis and his troops land in force there is little anyone can do to stop them. In the end it's left to Daniel to decide if he will try to stop Anubis - thereby breaking a cardinal rule of the Ancients.

A man breaks into Jack's house and hold him at gunpoint claiming that Jack ruined his life. Seven years ago he came upon an Ancient artifact at a garage sale that allows him to see all of SG-1's missions.