Several months after the Odyssey received Asgard upgrades, SG-1 traveled to Dakara in search of the Ark of Truth, an Alteran piece of technology capable of bringing an end to the Ori crusade. Unfortunately, shortly after they uncovered what turned out not to be the Ark, Ori fighters and troops arrived at the planet commanded by Tomin. After SG-1 killed the Prior, Tomin renounced the Ori and joined the Tau'ri. SG-1 and Tomin boarded the Odyssey, commanded by Lt. Colonel Cameron Mitchell, and set off for the Ori Supergate and the Alteran Home Galaxy. (SG1: "Unending", "The Ark of Truth")
The Odyssey cloaked immediately after reaching its destination in the Alteran Home Galaxy as to not draw the attention of the Ori. However, James Marrick used the Asgard computer core to create a Replicator as part of a plan to infect the Ori fleet with them and destroy their fleet. In an attempt to destroy the Replicator, Lt. Colonel Cameron Mitchell shot it with an Anti-Replicator gun, but the Replicator was immune to it and escaped to turn into a queen and replicate. The Replicator, as a queen, tied itself into a power conduit and started replicating a new army out of the Odyssey.
Meanwhile, teams swept the ship for the original Replicator, but by the time one was located and destroyed by Mitchell, there was already more than one. Lt. Colonel Samantha Carter started to search the program that created these new Replicators for the self-destruct that would destroy all of them at once, but four Ori warships launched an attack, forcing the Odyssey to jump to hyperspace so they couldn't be shot at while dealing with the Replicators.
The Replicators also took control of Marrick in order to get the self-destruct code so that it couldn't be used against them, and launched an attack against the Asgard computer core in order to gain full control of the ship while Mitchell went to find and destroy the Replicator queen. Mitchell managed to find the queen by following the other Replicators to the cargo bay where the queen was and set up a C-4 charge to destroy it as a distraction when one was needed. Marrick, controlled by a Replicator that attacked him before he could set it off, fought it out with Mitchell loosing until he pulled a Replicator attachment from Marrick's skull, causing Marrick to regain control of his body for a moment. Marrick told Mitchell where to find the self-destruct before losing control again. Mitchell blew the room up destroying the queen and Marrick, but seriously injuring himself in the process. He relayed the location of the self-destruct to Carter and she activated it just as a Replicator in the form of a human skeleton went after Mitchell. The Replicators were destroyed, saving the ship from one threat.
Meanwhile, unable to return fire, the Odyssey's shields were bombarded by Ori energy beam weapons. Despite being powered by a Zero Point Module, it was only a matter of time before the shields would fail. After twelve minutes of continuous bombardment and 144 hits, the Odyssey's shields finally failed. However, seconds before the final deadly shot was to be fired, the Ark of Truth was activated by Dr. Daniel Jackson, Vala Mal Doran, Tomin and Teal'c on Celestis and spread through the Prior staff to all Priors in the galaxy and the Ori withdrew. (SG1: "The Ark of Truth")
SG-1 took the Odyssey back to Earth where they used the Ark of Truth on a Prior being held captive there. The Prior staff spread the truth to every Prior in the Milky Way Galaxy and the truth about the Ori was revealed. Afterwards, the Ori army withdrew to their home galaxy under the command of Tomin, ending the crusade and SG-1 started going on normal missions again as the galaxy was now safe once again. (SG1: "The Ark of Truth")