After Sam receives an emergency call from geneticist Dr. Richard Flemming, the SGC learns that he has been working for Immunotech, a company owned by Adrian Conrad, who implanted himself with a Goa'uld symbiote in order to cure himself. Fleming has now gone missing and General Hammond orders Sam, Jonas and Teal'c to investigate. They head to Oregon where Fleming lived and worked and learn from the local Sheriff that Fleming isn't the first Immunotech worker to disappear. The locals are acting strangely and seem to suffer from memory lapses. What they eventually find is a town full of Goa'uld and NID seemingly aware of everything that is going on.

In a firefight with Jaffa, Teal'c takes a staff blast to the gut. Without his symbiote, he cannot regenerate as he once did. Daniel feels that he cannot remember something important, so he goes searching through the logs for any sign of his lost knowledge. Teal'c expresses his feelings that the Tritonin has made him weak.

When an SG geological exploration mission runs into deadly conflict with an indigenous Unas clan, Daniel gets Chaka to help seek an accord with it.

Bra'tac and Teal'c encounter a heavily armed enemy with shielding protecting him from Goa'uld weaponry who took out two Goa'uld personal guards. They barely manage to defeat him and bring him back to SGC for study, but this new threat poses a greater problem for the Tau'ri.

At the new Alpha site, Sam Carter and Selmak (the symbiote carried by Jacob Carter, her father) are working on a new weapon to defeat the Anubis superdrones when the planet is attacked by a fleet of Goa'uld ships. Carter escapes with the prototype weapon before the base auto-destruct is activated but finds herself being pursued by a superdrone.

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.

In a last ditch effort, O'Neill activated an Ancient weapon in the Antarctic to defeat Anubis. With Jack still in stasis in the Ancient outpost buried in Antarctica, SG-1 tries to contact the Asgard. Meanwhile their new leader, Dr. Elizabeth Weir, tries to decide what to do about a request for peace talks from the Goa'uld System Lords.

The Asgard fleet has managed to destroy the Replicator ship, with Carter aboard, but cannot contain the debris. Talks break down with the System Lords, ending in a Ha'tak being dispatched to test Earth's new defensive capabilities. The Prometheus waits to engage the incoming enemy, but Thor arrives in the Daniel Jackson, with Teal'c aboard. They enlist the help of Daniel and Jack, still in stasis, to remove the threat of the replicators to the new Asgard homeworld.

General O'Neill is still in the early days of commanding the SGC and faces a major problem when newly arrived Russian Col. Alexi Vaselov collapses in his quarters. Dr. Brightman's belief that Vaselof may be contagious seems correct when Daniel, who was with the Russian when he collapsed, apparently goes mad and tries to leave the base through the gate. O'Neill locks down the SGC but the problem isn't contagion: the essence of Anubis is alive and well and seeking a new host.

Dr. Lee is adapting a virtual reality chair for use as a training device. Teal'c thinks its current scenario is all too easy and agrees to work with them to make it more realistic. He enters the game scenario and is quickly "killed" at which point the chair shocks him. Lee says it must be part of its basic construct. As the scenario resets - it's an invasion of SGC by Goa'uld - Teal'c is repeatedly killed and shocked putting him in danger. The computer program is set up to learn after each scenario and the challenge for Teal'c increases at every turn. Daniel volunteers to enter the game as well to see if together they can find a way out.

Having obtained permission to live off the base, Teal'c rents an apartment, telling neighbors that he has recently arrived from Mozambique. He's under orders to keep a low profile but can't seem to help himself when it comes to helping his neighbors. He helps one who is about to be assaulted by three thugs, but it's his next-door neighbor who seems to need assistance. Krista is having problems with her boyfriend, Doug. Teal'c soon realizes that Doug is beating her and warns him that should he hurt her, Teal'c will kill him. It all becomes very difficult when Doug is found dead in Krista's apartment. Daniel Jackson soon after receives an offer - translate a Goa'uld text, and he will get ironclad evidence that Teal'c is innocent. Meanwhile, Carter is shocked when her boyfriend Pete Shanahan tells he asked for a transfer to the local police department and asks her to marry him.

When the Stargate gets beamed out of SGC in the middle of the night, Teal'c is stranded off-world. Dr. Jackson and Colonel Carter attempt to recover the gate.

With the threats of both the Replicators and the Goa'uld greatly diminished and the sister ship to the Prometheus, the Daedalus, now under construction, SG-1 is anxious to get a ride on the new ship. However, the mood is somewhat darkened by a phone call informing Dr. Jackson of Catherine Langford's death. After the funeral, Catherine's niece gives Daniel "a few odds and ends" that her aunt wanted him to have. Upon delivery it is discovered that almost her entire collection was shipped to Daniel's lab. He finds in one of her books a possible location of a ZPM, but scans of the area showed that it was no longer there. Daniel proposes that they use the Ancient's time machine to take it from Ra at Giza in 3000 BC.

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.

The team goes off-world and ends up in serious trouble. Meanwhile, Landry is faced with having to decide whether or not Vala can be trusted to remain at the SGC.

When an entire people may suffer the fatal wrath of a Prior of the Ori for not converting, General Landry orders Carter to try out an experimental device based on Merlin's technology to transport their whole village. The test works, but before they can activate it on a sufficiently large scale, an Ori force takes the village, wounds Sam and kills villagers near the Stargate before Vala's very eyes. Her husband, Tomin, captures her but claims to not love her. He is ordered, as punishment for being deceived by her, to re-educate her. Sam and Cam are able to activate the functioning part of the device, so their building is cloaked from the Ori, who threaten the village leaders and discover and arrest Teal'c. Even after the remaining villagers bow in submission, the Prior decides to destroy everyone since he couldn't find Sam, which makes Tomin doubt his faith, inform Vala, and confront the Prior. The villagers want to sacrifice Teal'c, but one leader stops them. Having seen the Prior destroy the village, Tomin sends Vala down, where she sees if Carter had managed, just in time, to get the device working...

Teal'c and Bra'tac are among the numerous victims -though only wounded- of several bomb attacks killing 32 men at a summit in the Jaffa settlement Dar Eshkalon. As soon as physically able, Teal'c swears to avenge them personally, suspecting the honor-less, ambitious warrior Arkad; General Landry refuses to sanction a killing mission without solid proof, but cannot stop Teal'c from going it alone. Bra'tac explains Arkad's sinister past to Daniel, including the possibility of murdering Teal'c's mother. Information from the resistance on another planet indicates Arkad is in league with the Ori and plans to attack Earth. Arkad comes to meet General Landry, offering to help defend Earth against the Ori, denying any part in the bombings, while defending Origin, incriminating a Jaffa sect. SG-1 is now ordered to find and stop at all cost Teal'c, who is using torture. But Teal'c, committed to killing Arkad, reaches his place, but is wounded, captured, and made to duel Arkad after it is confirmed he had killed Teal'c's parents.