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.

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?

The SGC is contacted by an advanced and embattled alien human civilization seeking military assistance, but their exact reasons for it become increasingly suspect.

While still dealing with the loss of Daniel Jackson the SGC is contacted by the Asgard who require assistance dealing with Anubis, who seems to have new shield technology that can repel Asgard weapons.

Ex-Vice President Kinsey comes to Jack informing him of the Trust's activities including what seems to be a plan for the Russians to reclaim the Stargate they lent to the United States. He decides to use Kinsey as their inside man with the Trust. Kinsey wears a wire for his meeting with the Trust to set up a meeting with a high-ranking Russian general. The plan goes south when the signals get jammed just as the Trust makes an astounding revelation to Kinsey and they beam out.

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.