It is time for Teal'c's son Rya'c to have his Prim'ta. Can Teal'c stop his son from being implanted with a Goa'uld and becoming a slave to Apophis?

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.

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?

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?

When SG-1 flees from an expedition with Col. O'Neill and some mysterious team member named Tyler, whom no one else knows about, stranded, the fitness of the team is questioned.

As the Goa'uld summit continues, Daniel finds himself face to face with Osiris. He fools him in the same fashion as he did with Yu, but cannot bring himself to cause the death of Sarah, Osiris's host. He remains to uncover information about the unknown master of Osiris. Lantash, having taken Lt. Elliot as a host, guides the rest of SG-1 in escaping the fallen Tok'ra base.

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.

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.

Following the death of a Jaffa on Earth and the disappearance of a prominent businessman, SG-1 starts an investigation into what remains of the Trust and into the actions of the Jaffa Nation. They discover that Ba'al is hiding on Earth after losing his forces to the Jaffa and that the Jaffa are secretly attempting his capture.

SG-1 blows up three transport ships in a row; Netan puts a price on their heads. General Landry grants the team members spare time on Earth. Daniel spends it researching in a library, where he meets a bounty hunter who tries to seduce him, then switches to her handgun... but is taken out by a bus. Sam gives a lecture on Air Force technological progress together with Dr. Bill Lee; a sniper nearly misses, but is taken out with an experimental weapon they'd brought along to demonstrate. Teal'c is injured by surprise at a Jaffa camp and successfully traps the killer to try again. Cam goes to his Kansas high school reunion and Vala succeeds in making him bring her along, pretending to be his accountant and partner. His still sexy former flame he'd believed out of his reach, Amy Vandenberg, is initially scared off by Vala, but, divorced and interested, explains she still has a secret crush on him. Alien bounty hunter Odai Ventrell assumes numerous classmates' appearances to kill him. Vala's failed rescue gets them both captured publicly, so he threatens to kill off reunion guests unless the other SG-1 members take their place, but they trick him using Chimera technology; they hope Netan's failure to eliminate them will rekindle the power struggle and Odai reacts surprisingly.