In a Tok'ra plan to wipe out the Goa'uld, Daniel goes undercover as Yu's servant to release a poison at a meeting of the system lords. Meanwhile a Goa'uld attack on the Tok'ra base leaves the rest of SG-1 with their hands full.
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.
A large asteroid is discovered on a heading straight towards Earth. If it hits, all life on Earth would likely be destroyed. SG-1 initiates a plan to repair a crashed Goa'uld cargo ship and deliver a naqahdah bomb to destroy the asteroid before it hits.
On an alien planet SG-1 discovers an inactive android is the only survivor of the destruction of her civilization. They bring her back to the SGC for study and manage to reactivate her. Things take a turn for the worse when she "makes" a replicator bug for Daniel.
Osiris engages in space combat with Thor over a violation of the protected planets treaty. Freyr arrives at the SCG bringing news of Thor's death and asking SG-1 to mount a rescue mission to retrieve an Asgard scientist from the planet in question. Upon their arrival Heimdall informs them that Thor still lives and has been taken captive by the Goa'uld. O'Neill and Teal'c transport over to the mothership to rescue him from the clutches of Anubis.
Master Bra'tac arrives with bad news: Teal'c's wife is deathly ill, and Teal'c leaves to be with her. Shortly thereafter, the gate is opened but nothing comes through. Then Carter discovers a very low power signal that is slowly building an overload powerful enough to destroy the Earth.
Anubis' weapon continues to threaten Earth. Various plans are tried until Jonas Quinn suggests something simple that just might work. Meanwhile, Master Bra'tac has discovered the planet from which Anubis is launching the attack. He, Teal'c and Rya'c journey there to put a stop to it.
Stargate Command discovers a Goa'uld Ha'tak in Earth orbit. Exploring, they discover it is the ship where Anubis briefly imprisoned Thor. At some point, Anubis' forces set the self-destruct and abandoned the ship, but something has halted the destruction and brought the ship to Earth. Jacob/Selmak opens the computer core so the team may learn more. Then the ship begins to descend towards Earth. SG-1 must discover what's going on before the destruction of the Ha'tak threatens Earth. And hopefully, escape the doomed ship themselves.
The SG-1 team travels to the Antarctic science station when the scientists there discover an ancient body in the ice. The age of the ice core samples would indicate that the body predates mankind. As they thaw the body, it comes to life. It's a young woman who they call Ayiana. As Ayiana gains strength, those around her all fall ill having contracted an unknown virus which they believe Ayiana carried. The new arrival also shows healing powers and can seemingly cure any illness just by touch. As she does so however she weakens to the point of death. In the end, only ...
A scientist named Fleming contacts SG-1. It seems the work of Immunotech has not stopped. The investigation carries SG-1 to a town in Oregon whose citizens lead curious double lives - right under the watchful eye of the NID. But all is not as it appears in a number of ways, and SG-1 must work quickly to prevent the NID's secret project from becoming a disaster for Earth.
Healed after being nearly killed by an Ancient virus, O'Neill finds himself held captive on a planet controlled by the Goa'uld Ba'al. O'Neill was brought here by the Tok'Ra symbiote that healed him and Ba'al wants to know why. When O'Neill can not give him an answer, he soon finds himself being tortured by Ba'al. As Carter, Teal'c and Jonas Quinn attempt to go through the Tok'ra records to find out where O'Neill was sent by the symbiot, O'Neill is killed and brought back to life many times by Ba'al and his only hope to keep his sanity comes in the form of the ascended...
Stargate Command is approached by representatives of Jonas Quinn's home planet seeking military hardware. Their world is divided into three territories and there is a long history of war among them. Jonas' country fears that the other two territories are about to sign a non-aggression pact thus making them vulnerable to attack. In return for arms, they are offering an abundance of nahquadria. SGC isn't about to get involved in what amounts to a civil war but there's another possible outcome when Jonas' one-time professor, Doctor Kieran, tells them of an underground ...
Told from the point of view of a stereo-typical scientist, Jay Felger (in love with SG-1). While on a standard science "baby-sitting" mission, SG-1 is captured by Khonsu (who is secretly Tok'Ra) in order to relay information about Anubis. Felger and fellow scientist, Simon Coombs disobey O'Neill's order to return to SGC and sneak onto Khonsu's ship. Khonsu's head Jaffa, Her'ak turns on Khonsu and kills him, keeping SG-1 to turn over to Anubis in the process. Felger and Coombs, manage to help SG-1 escape and return to the SGC.
The Tok'ra are forced to evacuate their newly established base under attack from the Goa'uld. They flee to the SGC's Alpha site. Tensions rise between the allied factions, the Free Jaffa, Tau'ri, and Tok'ra. Jacob and Selmac feel the end of the Tok'ra is near and Sam finds a Naquadah generator has been sabotaged to function as a bomb. Jack suspects the recently arrived Tok'ra and attempts to weed out the traitor.
SG-1 is negotiating a treaty with the inhabitants of Pangera. The have sometime miraculous to offer - a drug they call tretonin that can cure any ill. But there is a catch: the drug replaces the the user's immune system and must be taken forever. The Pangerans want specific world coordinates in exchange for the drug - and some of those places are the homes of powerful system lords. They won't explain why, but it clearly has to do with tretonin. Then the Tok'ra, called in to help solve the problem, make a startling discovery about the ultimate source of tretonin.
A television news crew has unearthed information about an Air Force project called "Prometheus". They believe it to be a generator, but know it uses Trinium, an element not found on Earth. In order to keep them quiet the Air Force allows them to film the X-303, a spaceship based on Asgard technologies, otherwise known as Prometheus. Things turn south when the news crew arm themselves and hold the Prometheus, as well as Sam and Jonas, hostage.