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.

A Prior of the Ori has established an ever-growing forcefield on a Jaffa-controlled planet called Kalana. A minor Goa'uld named Nerus, 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 Ba'al is hiding on Earth after losing his forces to the Jaffa and that the Jaffa are secretly attempting his capture.

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.

Based on the information Vala gave them, SG-1 travels to the planet where Merlin may have hidden his secret weapon to defeat ascended beings. There they find an appropriately medieval village and learn that Merlin kept a library there. The locals have never been inside owing to a curse on anyone who dares enter, but SG-1 finds a way in. Once inside, they find a secret chamber that may reveal the location of the weapon. The SGC, meanwhile, has located the Ori's Supergate. Sam's attempt to get control of it is too late, and four Ori ships make their way through. In the ensuing battle, much of Earth's fleet is destroyed, and the future of several SGC members is left in doubt.

As the Ori invasion continues, Vala and Daniel must deal with their leader, Vala's young daughter, who is rapidly aged by the Ori to serve their purposes.

SG-1 is caught in the middle of a war after the Jaffa use a powerful weapon to kill 10,000 Ori followers.

Cameron Mitchell must go undercover inside the Lucian Alliance to find the location of the hijacked Odyssey.

Stargate Command gets a video message from Vala's extremely unreliable father, Jacek, on the planet Robak; he claims to know about the late Arkad's plans to attack and blow up Earth, even about the several cloaked, Naquadah-laden cargo ships in orbit, and offers details in exchange for sanctuary. General Landry asks Dr. Lam to help him resume contact with her mother, Kim, his ex-wife. Even after the cargoes are found and blown up, Vala abhors her dad's entry. The general asks her to go easy on him, realizing that he, too, neglected his daughter because of his career, even if Jacek's neglect was just criminal. When Cam and Daniel go tell Jacek he shouldn't scam people, he tricks them into talking to Vala for him. Vala goes over just for catharsis, telling him she's through picking up the pieces of his tricks, and he certainly keeps scamming - as Daniel also finds - even with Terak, a Jaffa from an escaped cargo ship, who hopes to sell the Naquadah. When they are apprehended, Jacek promises to help track it and override the rigging of the cargo ship. The Jaffa wait for Jacek and Vala, intending to eliminate them now that Terak is gone, but SG-1 saves them. Since there never was an override, Jacek cheerfully flies away alone in the cargo ship, ignoring that his treachery was anticipated: it's a decoy.

General Landry accompanies SG-1 on a mission to collect the knowledge of the Asgard. When the Ori show up, however, Sam is forced to evacuate the crew. Landry and SG-1 stay aboard, but are stuck helpless in a time dilation field for decades.