SG-1 discovers a box that they believe contains the Ark of Truth while digging on Dakara, but before they can open it, Ori soldiers arrive, led by Tomin. Daniel (Michael Shanks) tricks them into opening the box, but it is revealed to be a fake. When Tomin is ordered by a Prior to kill them, he refuses, and Mitchell kills the Prior, whose powers were being blocked by the Anti-Prior device. Shocked at the death of their Prior, the Ori soldiers surrender with Tomin returning to Earth with SG-1 where he resides at the SGC for a time.
Back on Earth, General Landry and Mitchell meet James Marrick, an IOA representative sent to interrogate Tomin due to the fact that the original IOA representative, Richard Woolsey is now working for the Atlantis Expedition. When Daniel Jackson realizes that the Ark is still in the Ori galaxy, Marrick is assigned to accompany them on board the Odyssey through the Supergate. In the Ori galaxy, a member of the anti-Ori resistance tells the team that according to legend, the Ark is on Celestis, the Ori capital. When SG-1 beams down to the planet, Marrick activates the Asgard computer core which alerts the Ori to the ship's location.
Upon being alerted by Major Kevin Marks of what's going on, Mitchell and Carter beam back to the Odyssey and discover that Marrick has used the core to build a Replicator, intending to plant it on an Ori ship and let it spread to their entire fleet. When Mitchell attempts to destroy it with an anti-Replicator Gun, the replicator escapes, and Marrick reveals that the IOA removed that weakness from the design, although conventional weapons are sufficient to destroy individual replicators. Marrick implies that a shutdown code has been included as a failsafe, but claims he does not know what it is. He is placed in the ship's brig and falls victim to the Replicators who later make their way into the brig, resulting in Merrick becoming a Human-Replicator hybrid. With several Ori ships approaching, Mitchell attempts to beam Daniel, Teal'c, Vala, and Tomin up from the planet, but the replicator takes over the system and keeps Mitchell from doing so. With no other option, the Odyssey jumps to hyperspace to escape, leaving the others on the planet.
Daniel finds the Ark in a set of catacombs, and after several ground tremors, brings it to the surface. When the team emerges, they are ambushed by Ori warriors, and Teal'c is shot in the back while the others are captured. When they are brought to the city, Vala discovers that the Ori were indeed killed by the Sangraal during the events of The Shroud. Adria has ascended and taken over all of their power. Teal'c, who has been walking toward the city of Celestis since he was shot, collapses due to his wound within sight of the city. He is subsequently revived by Morgan le Fay and continues on to free Daniel. Morgan then arrives in Daniel's cell (initially in the guise of Merlin) and tells him if he can expose one Prior to the Ark, the others will be turned by a link in their staffs. This will weaken Adria enough for Morgan to stalemate her.
In the meantime, a Prior arrives on Earth, offering a last chance to convert to Origin. When General Landry refuses to even listen to him, the Apollo detects a fleet of Ori motherships waiting on the edge of the solar system. On the Odyssey, Marrick is attacked by Replicators who infest his body. In the ensuing battle, Mitchell is able to briefly disable the Replicator connection to Marrick's brain who then informs Mitchell the shut down code for the Replicators is located on the other side of the crystal used to create them. Mitchell activates an explosive charge which kills Marrick. Mitchell informs Carter who activates the shut-down command, deactivating the Replicators.
When the Ark is activated and opened, the Doci is caught by the beam and made to see that the Ori are not gods and spreads this belief to all of the Priors in the Ori galaxy and through them their followers. With Adria now in a weakened state, Morgan is able to engage her in an eternal battle. SG-1 exposes the Prior on Earth to the Ark, transmitting the knowledge about the Ori to all of the Priors in the Milky Way, and thus turning all known Priors in the Universe.
In the aftermath, Tomin departs for the Ori galaxy as the new leader of his people, he and Vala agreeing that, while the Ori themselves were liars, Origin itself has a worthwhile message. Tomin asks Vala to come with him, but Vala apologizes and says that she feels her place is with the SGC. Over Daniel's objections the Ark is taken to Area 51 for study while SG-1 later prepare for another new mission through the Stargate.
What does Marrick become?
Human-Replicator hybrid