SG-1 discovers a box that they believe to be the Ark while digging on Dakara, but before they can open it, Ori soldiers arrive, led by Tomin. Daniel 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 is able to kill the Prior, whose powers are being blocked by the Anti-Prior device.

Back on Earth, General Landry and Mitchell meet James Marrick, an IOA representative sent to interrogate Tomin. 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. When SG-1 beams down to the planet, Marrick activates the Asgard computer core which alerts the Ori to the ship's location.

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. 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, decides to bring it to the surface. When the team emerges, they are ambushed by Ori warriors, and Teal'c is shot in the back. When the rest 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 from his back wound within sight of the city. He is subsequently revived by Morgan le Fay and continues on to free Daniel. Morgan le Fay then arrives in Daniel's cell and tells him if he can turn one Prior, the others will be turned by a link in their staffs. This will weaken Adria enough so that Morgan will be able to defeat 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 informs Mitchell about a shut down code for the Replicators, located on the other side of the chip used to create them.

When the Ark is activated and opened, the Doci is caught by the beam and made to believe that the Ori are not gods. In Adria's new weakened state, Morgan is able to engage Adria in an eternal battle, similar to Oma Desala's eternal battle with Anubis in Threads. 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 powerful message (Vala personally recommends omitting the part about burning people alive for disagreeing with the religion). Tomin asks Vala to come with him, but Vala apologises and says that she cannot, feeling that her place is with the SGC. Despite Daniel's objections, the Ark is taken away to Area 51 to study, leaving SG-1 to travel to another planet and see what wonders (and treasure, in Vala's case) it holds.