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.

The SG-1 team awake to find they have lost their memories. They believe they are workers in an underground power station. They are told that they are helping to preserve life during an ice age. In truth, they are slave labor to a huge domed city above. When Teal'c starts to recover his memory and is given another amnesia treatment, he forgets his Kelno'reem and starts to die. Will the others recover their memories in time to save him?

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.

On a routine mission, SG-1 encounters a civilization desperate to be freed from the clutches of a Goa'uld. While on the planet, Jonas falls ill and is suspended from active duty. His mysterious illness is diagnosed as a brain tumor but gives him the unbelievable ability to glimpse the future, a future where O'Neill and SG-1 are walking into a trap!

Anubis's super weapon has been put out of commission, but Yu's fleet has been diverted to the other side of the galaxy by Yu himself, allowing Anubis to escape into hyperspace. Jonas has been captured by Anubis and Daniel is still aboard Anubis's ship, evading capture. Anubis uses the mind probe on Jonas, learns of Naquadria, and begins his attack on Kelowna. The Kelownans seek aid from the SGC. Jack and Sam arrive on Langara to discover that the Kelownans have given Anubis Naquadria in order to secure their safety. They communicate with Daniel who is attempting to free Jonas. Teal'c has convinced Yu's first prime to seek a new leader of the System Lords, Ba'al.

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.