The discovery of the Stargate creates a war between two nations on the planet Tegalus with Daniel in the middle of it.

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.

With a new commander of the SGC comes a new leader of SG-1, Lt. Col. Cameron Mitchell, a former fighter pilot who flew an F-302 in the battle over Antarctica. However, he is deterred by the fact that all the other members of SG-1 are leaving for other ventures: Teal'c to manage the Jaffa Nation, Carter to Area 51 for alien R&D, and Dr. Jackson to Atlantis as an Ancient expert. Mitchell endeavors to keep the members of SG-1 for himself, but they are increasingly tough to convince.

Vala leads SG-1 to a planet which the Priors have visited with a plan to keep them from worshiping the Ori. Once there she reveals that the symbiote that once held her ruled over this planet. She feels that keeping them in allegiance to her will hinder the spread of Origin to this world.

SG-1 investigates a planet that is said to be the home of the Warriors of Sodan, a legendary tribe of Jaffa said to have not served the Goa'uld in 5,000 years. In an encounter with the warriors, Mitchell deals a deadly blow to one of the Sodan and is captured and taken to their village. There he awaits a battle to the death as punishment for his crime.

The Ori unleash a deadly plague on Earth, prompting a powerful ally from SG-1's past to come to their aid.

The plague continues to spread among the US population and the President has quarantined the nation. Teal'c is pleading with the Jaffa High Council to reject Origin, but Gerak arrives, having been transformed by the Ori into a Prior. Cameron and Daniel seek the blood of the Prior that caused the plague in order to cure it, but have once again been captured by the Sodan.

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...

During a failed experiment, Samantha is transported into a parallel universe where she cloaks Earth to save it from an Ori attack. Getting back to her own universe is not met with sympathy.