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.

Former Colonel Harry Maybourne comes to Jack with a proposition: Jack gets him a presidential pardon and Harry shows them the advanced weapons cache that Simmons was trying to get to. They go through with the deal, but Harry attempts to double cross SG-1. He manages to get through the portal leading to the cache, but with one unexpected item, Jack. They find themselves in a field and Harry's zat is missing. Jack, however, still has his P-90. Harry reveals that they are not at a weapons cache, but rather a utopia. He meant to live out the rest of his life there and believes that there is no way back.

The US and Russia reveal Stargate Command and its operations to representatives of the other permanent members of the United Nations Security Council.

SG-1 investigates a planet that is said to be the home of the Warriors of Sodan, a legendary tribe of Jaffa said to have not served the Goa'uld in 5,000 years. In an encounter with the warriors, Mitchell deals a deadly blow to one of the Sodan and is captured and taken to their village. There he awaits a battle to the death as punishment for his crime.

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.