The ark of truth is an Ancient device programmed to un-brainwash the followers of the Ori, evil god-like beings who gain strength from the worship of their devotees. Guided by the visions of Daniel Jackson (Michael Shanks
), apparently remnants of his shared consciousness with Merlin, SG-1 searches for the ark. They fly the Odyssey through the supergate to the Ori galaxy. Accompanying them are Marrick (Currie Graham
), a representative of the IOA, the international body that oversees the Stargate program, and Tomin (Tim Guinee
), a renegade commander of the Ori forces. Tomin, like Teal'c (Christopher Judge
) in the early seasons of Stargate SG-1
, is tormented by the wrongs he did for his evil masters. Teal'c pitilessly tells Tomin that Tomin will never forgive himself, but he must nevertheless work to help others.
Working on a tip from the anti-Ori resistance, SG-1 beams down to the Ori planet Celestis to look for the ark, but Lt. Cols. Carter (Amanda Tapping
) and Mitchell (Ben Browder
) return to the Odyssey when they learn that Marrick has locked himself in with the Asgard core, an advanced system installed by Earth's Asgard allies. Before they can get to him, Marrick installs a chip in the core and launches a program that synthesizes a Replicator. (Replicators are self-replicating machines that try to take over any ship or world they encounter.) The Replicator, naturally, escapes into the ship, while Marrick explains that the IOA never believed that SG-1 would find the ark. Unleashing Replicators is the IOA's plan to defeat the Ori's followers.
While Carter and Mitchell struggle with the Replicators for control of the Odyssey, Jackson, Teal'c, Vala (Claudia Black
), and Tomin descend into a system of tunnels pointed out to Jackson by Merlin. They find the ark, but before they can return to the beleaguered Odyssey, the Asgard core attracts several Ori motherships. The Odyssey jumps to hyperspace to escape, leaving the party on Celestis behind -- along with the ark. The ark and all but Teal'c are captured and taken to the Ori city.
Meanwhile, an Ori prior has come to Earth to remonstrate with General Landry (Beau Bridges
); the general locks him up. Later, Earth is threatened by approaching Ori motherships.
Teal'c, wounded and left for dead on Celestis, goes in search of his friends. As he hobbles across a spectacular mountain range, the head prior torments Jackson and Tomin. (Vala looks tormented too, but Tomin's screams seem to be the cause of her misery.) Vala is taken to see Adria the Orici (Morena Baccarin
), who has ascended. Adria confirms that as SG-1 hoped, the Ori have been destroyed. Unfortunately, Adria has assumed all their power.
Alone in his cell, Daniel Jackson has another vision of Merlin. He realizes that all along, he has been seeing not Merlin but Morgan le Fay (Sarah Strange
), the ascended Ancient who tried to help SG-1 find the Sangraal (the Ancient weapon that destroyed the Ori). Morgan tells Jackson that they need to expose just one prior -- any prior -- to the ark of truth; once one prior is disinfected, the truth (that Adria and the Ori are false gods) will spread to the others through their staffs. He asks her for more help, but she assures him she's doing all she can.
Outside, Teal'c has reached the wet plain around the Ori city, where he collapses. His wound is healed by an ascended being (presumably Morgan le Fay). His strength returns and he enters the city to rescue Jackson and the others.
Marrick, aboard the Odyssey, has apparently been consumed by the Replicators. Carter searches the Asgard core for the code that Marrick hinted would shut down the Replicators. The Replicators drop the Odyssey out of hyperspace; the Ori ships catch up quickly and start shooting. Mitchell finds the Replicator queen and plants a bomb nearby. He's interrupted by a torn-up Marrick who's controlled by a large Replicator embedded in his back. Mitchell and Marrick fight. When Mitchell pries the Replicator's prong out of Marrick's head, Marrick comes to himself and reveals that the Replicator shut-down code is on the back of the chip he installed in the Asgard core. Then the Replicator regains control of Marrick and Mitchell electrocutes him. He finds the detonator for the bomb he planted near the queen and radios Carter to tell her where to look for the shut-down code. As Mitchell sets off the bomb, Marrick is coming after him again.
The bomb destroys Marrick's body and, we assume, the Replicator queen, but Carter and her team, busy fighting off the remaining Replicators, have little attention to spare to find the shut-down code. Wounded and exhausted, Mitchell watches in horror as the Replicator that controlled Marrick reforms itself in the shape of his skeleton, while a swarm of smaller Replicators approaches from the other direction.
In the Ori city, Vala, Jackson, Tomin, and Teal'c try to activate the ark. They succeed as the head prior enters the room. He's instantly deprogrammed and collapses in shock when he realizes how much harm he's done in the name of the Ori. As Morgan le Fay promised, the truth is infectious, and it spreads to the other priors in the Ori galaxy. Adria, weakened by the loss of the priors, is now vulnerable, and Morgan attacks her. They disappear in a swirl of ascended-being-light.
Carter finds and executes the Replicator shut-down code just in time to save Mitchell. Mitchell tries to surrender the crippled Odyssey to the Ori ships that are still attacking, but the priors aren't interested and keep shooting -- until, suddenly, they stop. The ark's infectious truth has spread to the ships.
Back on Earth, General Landry returns the captive prior's staff, then exposes him to the ark. The staff communicates the truth to the priors in the Ori ships that are poised to attack, and the Earth is saved.
Vala talks with Tomin as he prepares to go home and assume the leadership of his people. She declines to go with him, saying she hopes her place is on Earth -- with SG-1.