Tragedy reunites Teal'c with his son, who blames him for the death of his mother. O'Neill and Carter launch a risky plan with untested technology when Earth comes under attack by the Goa'uld.
Carter must find a way to save Earth from total destruction at the hands of the Goa'uld, who have turned the Stargate into a doomsday bomb. Rya'c joins his father on a mission to destroy the Goa'uld weapon.
SG-1 attempts to salvage a Goa'uld mothership that has been mysteriously abandoned in space near Earth. Unfortunately, the ship crashes in the ocean. SG-1 discovers that Thor's consciousness is still in the central computer.
The Antarctic team investigating the site where the second Stargate was found discovers a woman frozen in the ice. When she inexplicably recovers, the team realizes they have finally come face-to-face with an Ancient. The team starts to suffer the effects of a deadly virus and while the woman helps to heal the infected, it becomes clear that it's taking a toll.
Carter, Teal'c and Jonas investigate the death of a scientist with connections to the Goa'uld, and find a small town whose citizens harbor a dark secret.
O'Neill has been captured by Ba'al but is being held in a fortress too well protected for Stargate Command to help. However, Jonas believes that Lord Yu might be persuaded to lend assistance. Meanwhile, O'Neill is helped through his ordeal by Daniel, who although forbidden from taking action tries to provide comfort.
The Kelownan government contacts the SGC, offering to exchange naqahdriah for advanced technology. Jonas's old professor asks him to help a secret resistance group and prevent a world war.
Dr. Felger worships SG-1, and when he has the chance to rescue them from a Goa'uld mothership, he does not hesitate.
The Jaffa rebellion, the Tok'ra and their base commander Malek, and Stargate Command are temporarily forced to share Earth's Alpha Site (a secret refuge) when the Tok'ra are attacked. Suspicion between the Tok'ra and the Jaffa turns hostile when a series of murders occurs.
SG-1 visit Pangar, a planet once ruled by Ra. The Pangarans offer a wonder drug called Tretonin in exchange for gate addresses, but fail to mention that the drug is produced by using the progeny of the former Tok'ra queen Egeria. The drug also destroys the user's immune system, causing a crisis when supplies ran low. SG-1 calls in help from the Tok'ra Malek and Kelmaa. After Egeria is freed by the Tok'ra Kelmaa, she tells the remorseful Pangarans how to free themselves from the tretonin.
A reporter has information about the Stargate Program and threatens to broadcast it on television. The SGC offers a deal to allow her access to the Prometheus on the condition that nothing is aired until the Stargate Program is made public. However, the camera crew turns out to be rogue NID agents and take over Prometheus.
The Asgard have called all the Replicators in the Asgard galaxy to one planet, Hala, but the time dilation device that was meant to trap them on the planet forever has failed to activate. The Asgard want SG-1 to use the Prometheus to find out why. Unfortunately, what they find is that the Replicators have accelerated time and evolved to human form.
On a deserted planet designated P9X-391, SG-1 discovers a piece of Ancient technology. When it is moved to Earth for study, people begin to have inexplicable hallucinations.
Colonel O'Neill is charged with the murder of Senator Kinsey, and the rest of the team must uncover a conspiracy in order to clear his name.
Maybourne offers to help the SGC find a cache of advanced alien weapons, but he is not telling them everything he knows.
The Russian team discovers a planet where Nirrti has been experimenting on the human population to create the perfect host.
The Americans and the Russians reveal the existence of the Stargate to the British, Chinese and French governments due to the mounting threat by Anubis. Senator Kinsey tries to use the meeting to hijack the program, but Hammond has a card up his sleeve.
SG-1 finds a wrecked spacecraft whose crew claims to have been fighting off aggressive aliens ever since they crashed. It later turns out that the crew are in fact prisoners of the Serrakin ship Ceberus. The Serrakin are an advanced race who once helped free the human Hebridans, descendants of the Celts, from the Goa'uld millennia ago. Since then, the two peoples have lived together in a largely harmonious society on the planet Hebridan.
Teal'c finds himself jumping between different realities of Earth and the planet Kresh'ta, where a meeting of 108 Jaffa rebel leaders are ambushed by the Goa'uld System Lords. Only Daniel seems to display any understanding of reality.
On the maiden flight of the finished Prometheus, the reactor overloads, and SG-1 must find the Stargate buried on the alien planet Tagrea in order to obtain spare parts from Earth. Tagrea was once ruled by the Goa'uld Heru-ur, and the memory of his occupation was so traumatic that the Tagreans buried their Stargate and wiped out all traces of their earlier history, so as to make a new start. Despite opposition from xenophobic elements of the Tagrean military, the progressive Chairman Ashwan assi
SG-1 finds a planet where the population worship Ba'al and work in the mines to provide his representative, Lord Mot, with a tribute of naqahdah. SG-1 intends to stop him, but things get complicated when Jonas starts seeing visions that could kill him.
Daniel Jackson contacts Jack and tells him that Anubis has located the Eye of Ra, an enormously powerful weapon. SG-1 heads for Abydos to rally their old friends against Anubis's fleet, while Daniel confronts Anubis and learns the terrifying truth about him. While trying to find the Eye, SG-1 learns that there is a Lost City of the Ancients that may hold the key to defeating Anubis once and for all.