While still dealing with the loss of Daniel Jackson the SGC is contacted by the Asgard who require assistance dealing with Anubis, who seems to have new shield technology that can repel Asgard weapons.

A group of nomads on an alien planet find Daniel Jackson naked in the middle of ruins and take him in. Jonas translates the tablet Daniel said was important and discovers that it describes the last city the Ancients were building before the plague. He surmises that the list of addresses Jack put into the computer while storing the Ancient data were Ancient outposts in temporal order. Thus the last of the addresses should be the "City of the Lost". SG-1 visits the planet and happens upon the nomadic people, now inhabiting the ruins of the Ancient city. There they find Daniel, but discover his memory is gone. They must recover his memories in order to discover the secret to defeating Anubis.

General O'Neill is still in the early days of commanding the SGC and faces a major problem when newly arrived Russian Col. Alexi Vaselov collapses in his quarters. Dr. Brightman's belief that Vaselof may be contagious seems correct when Daniel, who was with the Russian when he collapsed, apparently goes mad and tries to leave the base through the gate. O'Neill locks down the SGC but the problem isn't contagion: the essence of Anubis is alive and well and seeking a new host.

Daniel Jackson, who was left behind fighting off Adria while the other SG-1 members escaped through the Stargate, is found working as a Prior: the best in the business, who doesn't need to use any threats to talk people into conversion to Origin. Hoping there is still some of his personality left, the team (plus General Jack O'Neill) kidnaps him. Daniel explains how he temporarily has Merlin's personality and knowledge in himself, and had deliberately allowed Adria to turn him into a Prior, while delaying to finish Merlin's weapon she'd wanted, meanwhile hoping to get an Ori ship for Earth's side. But time is running out, since the team took unexpectedly long to capture him. Still, the generals, Carter, and Vala are most reluctant to go along with releasing him and opening the wormhole he needs to bring the weapon through. Even the White House wants to kill him, or at best, keep him in stasis until he is reverted to his human nature by Merlin's genetic manipulation. But then his plan is wasted- unless the others can be trained to do it in his place (so only they are at risk, not the entire galaxy in case Daniel is Adria's Trojan Horse). After giving them the necessary information, Daniel suddenly frees himself while Richard Woolsey is with him and takes control of a space ship after beaming up Jack too, just after the others have undertaken their mission to Adria's lair, where Daniel, about to be genetically reverted, arrives just in time to tip the balance in their favor.