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.
Upon finding Merlin's testing grounds, Dr. Jackson, Teal'c, Col. Mitchell, and Vala uncover the hidden treasure including a book that tells the story of the Ancients coming to Earth from another galaxy and a strange alien device.
Daniel and Vala have used the Ancient device to inhabit the bodies of people in the Alterans' home galaxy. They have been taken by a prior of the Ori to meet the Doyen, one who speaks with the Ori, their gods. Daniel surmises that the Ori are what the Alterans who became the Ancients left behind and have ascended in a similar fashion, but without the restrictions.
Vala returns to SGC upon having been separated from Daniel for a little under an hour. The effects of the bracelets have not diminished even though they have been removed. In order to get the effects reversed, Mitchell, Jackson, and Vala must deal with many people that Vala has used over the years to gain favors.
Vala leads SG-1 to a planet where 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.
A prior of the Ori has established an ever-growing forcefield on a Jaffa-controlled planet. A minor Goa'uld, but also the one who engineered the multiple gate connections required for the defeat of the Replicators, comes to the SGC with information on the event and offers his help.
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 Baal is hiding on Earth after losing his forces to the Jaffa and that the Jaffa are secretly attempting his capture.
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 hundreds of 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.
In an attempt to observe what may be an undiscovered black hole, Carter is sent to the wrong planet. She returns with this information and begins diagnostics on the dialing computer. When they find that nothing is wrong on their end, Carter theorizes that the gate is keeping people out by redirecting them to a random planet. She cracks the code keeping them out and SG-1 goes to investigate the planet.
A prior has convinced Gerak, leader of the Jaffa Nation, into following Origin. He is attempting to make Origin a state religion for the Jaffa. Teal'c and Bra'tac attempt to make a case against the Ori, but to no avail. Meanwhile, a "prior plague" has breached SGC and spread to the rest of Colorado.
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.
Multiple SG-1 teams begin coming through the gate, each one from a different parallel universe. Carter teams up with Martouf (Tok'ra), who in his reality joined the SGC, and Kvasir (Asgaard) to try and figure out a way to repair the damage that was done so that more alternate SG-1 teams do not become stranded.
Leader of the Hak'tyl and their representative on the Jaffa High Council, Ka'lel has fallen in with those who work against a democratic Jaffa nation. Things worsen when she incapacitates and turns a well-spoken brother Jaffa who promoted democracy. Bra'tac comes to Hayes and SG-1 for help in finding a now missing Teal'c and uncovering the shadowy dealings in the Jaffa High Council. On Earth, Mitchell gets an old friend of his into a hospital where alien-based technology is used; hopefully, the advances they have made will be able to cure what ails him.
A contact within the Rand Protectorate comes to Earth with news that the Ori have given his people a superweapon to use against the Caledonian Federation in exchange for their conversion to Origin. SG-1 plans to turn the people from their newfound religion and destroy the superweapon.
While investigating the source of an addictive corn-like crop, SG-1 becomes involved in a firefight. They are forced to fall back to the gate, but as Daniel is dialing both the Stargate and the DHD are beamed away.
The SG-1 members grumble at the "honour" to host some international representatives of a powerful commission on a tour of a research base on another planet. Suddenly a project concerning voracious beetles intended to control an addictive plant they hardly deemed worthy half a minute suddenly turns dangerous: once fed a bit of meat, they prove unstoppable carnivores, escape and cause the base to be automatically quarantined, and later even to self-destruct - the surviving humans are surrounded, without means of communication, so earth will presume them dead and ...
When Samantha finally manages to start a device made by Merlin, it unfortunately renders her and colonel Mitchell invisible by transporting them to a parallel dimension. They must wait to be able even to manifest themselves till doctors Jackson and Bill Lee figure things out from the display the device presents in the language of the Ancients. Meanwhile Teal'c and SG-12 travel to the planet where a whole Sodan village is exterminated by its own hero Volnek, who was turned evil by a prior as a punishment for their 'disrespect' to the Ori - and find he sabotaged the ...
As a result of a communication technology simulation Sam didn't even expect to work, Vala is able to possess Daniel's body long enough to tell how she awoke on an Ori-devoted planet, where she married the kind native Tomin when realizing she was pregnant although she couldn't imagine how or by whom, but found out a prior healed his old crippling wound so he could be conscripted to a huge army the Ori were preparing, while building a large fleet, for a crusade against the unbelievers. Meanwhile on earth, the Russians announce they won't prolong the treaty to lend the ...
Since the weapon Merlin once devised against ascended beings seems the human race's best change to resist or even defeat the Ori, SG-1 travels by stargate to a medieval society in a place called Camelot where the local Arthur epic (differerent from earth's romanticized traditions) confirms its location should be found in a forbidden library guarded by a Black knight. When they are beamed up to earth's super-star-ships about to try stopping the Ori-fleet passing a super-gate, Daniel and colonel Mitchell decide to have themselves beamed back inside the library, but on ...