General Hammond returns to SGC to take Dr. Jackson with him on a trip to Atlantis onboard the Prometheus. In the middle of their trip, the Prometheus picks up a distress signal and Hammond decides to investigate. Things get sticky when a Kull Warrior takes control of the Prometheus, leaving Hammond and his crew, minus Daniel Jackson, behind in a damaged Alkesh.
Ex-Vice President Kinsey comes to Jack informing him of the Trust's activities including what seems to be a plan for the Russians to reclaim the Stargate they lent to the United States. He decides to use Kinsey as their inside man with the Trust. Kinsey wears a wire for his meeting with the Trust to set up a meeting with a high-ranking Russian general. The plan goes south when the signals get jammed just as the Trust makes an astounding revelation to Kinsey and they beam out.
A man breaks into Jack's house and hold him at gunpoint claiming that Jack ruined his life. Seven years ago he came upon an Ancient artifact at a garage sale that allows him to see all of SG-1's missions.
After a long absence Jacob Carter returns to the SGC to tell Jack that the galaxy is under threat of takeover by the Replicators. The Goa'uld are under attack from the Replicators and are quickly being eliminated. Baal's armies are being destroyed and he arrives at SGC to suggest they work together to defeat their common enemy. Carter's doppelganger, RepliCarter, is leading the attack and she has kidnapped Daniel Jackson in the hope of learning of any weapons the Ancients may have created that could defeat them. Carter gets help from an unexpected source - the Ancient...
Sam and Jacob are on the planet Dakara trying to configure the Ancient's device to destroy the replicators once and for all, helped partly by Baal and Daniel who succeeds in freezing the replicators by manipulating Carter's duplicate.
Daniel finds himself in a strange time and place - a diner where Oma is working as a waitress. She gives him a clear choice - he can choose to die or to ascend but if it's the latter, he will not be able to help his friends fight Anubis, who has yet to be disposed of. He strikes up a conversation with another patron, Jim, who has his own take on the situation. Sam meanwhile decides the time has come for her fiancé to meet her father Jacob. Jacob is not well however, something he has kept from Sam for several weeks. After Pete surprises her - he thinks he's found the ...
With the threats of both the Replicators and the Goa'uld greatly diminished and the sister ship to the Prometheus, the Deadalus, 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 ...
SG-1 has changed the course of history and made SGC virtually non-existent. Doctors Carter and Jackson have helped Brigadier General Hammond to find the Antarctic Stargate, but are not being allowed to help any further. They help Jack to power up the time machine, and he gets Hammond to allow them on the mission to find Teal'c.
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.