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Vala returns to the SGC using the same body shifting device seen in "Avalon (2)." In a shift, she returns in the body of Daniel Jackson. She says she has important information to convey to the SGC. However, she digresses into a long diatribe about her time on her distant planet and its people's struggle there with the Ori, and she finally describes the new great threat to Earth. Also, Vala tells them of an underground resistances group on this planet that opposes the Ori.

Carter tries to figure out what a strange device found in Merlin's cave does, after Dr. Lee failed to figure it out after six months. Carter finds something interesting, which unfortunately causes her and Mitchell to be transported to an alternate dimension. They can see and hear those around them, but no one can hear or see the two.Teal'c, meanwhile, goes with SG-12 on a mission to check on the Sodan, after a distress message is received. Once there, they find Volnek has been affected by a Prior and is now killing everyone in his group in a crazed frenzy and madness, after actually having died.The two story lines converge when Mitchell decides to go in his "out of sync" state with a second SG team set to rescue Teal'c and SG-12.

When an SG team returns with a corn-like food stalk that has addictive, and mind altering effects, SG-1 is sent to investigate. They head to the planet where the corn-like food, known as kassa, is grown, but their investigation provokes an angry response from the Lucian Alliance that controls the food. While under fire from the alliance, and as they are attempting to dial home, the Stargate and DHD suddenly disappear, leaving SG-1 trapped.After SG-1 is later rescued from the alliance by Earth's newest ship, the Odyssey, SG-1 tries to find out who stole the gate. Gen. Landry decides to seek help from the Goa'uld Nerus. Nerus eventually breaks down, after some creative torture techniques by Gen. Landry, and tells them who stole the gate on the alliance's planet and several other gates as well.The answer shocks the team, and poses many additional impossible challenges to getting the gates back, but reinforces the need that they do, for the sake of Earth's future existence.

The SGC learns that the Caledonian's arch enemy, the Rand government, has been visited by a Prior, who has offered them great weapons to defeat the non-believing Caledonians. The main weapon is a satellite platform which can destroy all of the Caledonians. The Prior is slowly giving the Rand government instructions on how to construct the satellite platform. There may still be time to destroy the weapon, as SG-1 sees that such a weapon could eventually be used against other non-believing worlds, too.SG-1 decides to take the Prometheus with them in an attempt to destroy the weapon, before its completion. Daniel travels through the gate to try to convince the planets leaders the evil of the Ori. However, Daniel is thrown jail as an enemy of the State, and the Prometheus receives a deadly surprise, once it arrives.

Ba'al brainwashes members of the Jaffa High Council to thwart their move toward democracy. Cameron Mitchell faces a tough decision when he learns that an old friend is about to die.

Earth now faces a world wide Pandemic caused by the Ori. However, Orlin's return to help Sam, and Earth, brings great relief, at least until they learn the downside to Orlin. Part of the SG-1 team is tasked to get the blood of the Prior that caused the infection, in hope it may lead to a cure to the plague.

A Prior has convinced Gerak, leader of the Jaffa Nation, into following Origin. Teal'c and Bra'tac attempt to make a case against the Ori, but to no avail. Meanwhile, a plague released by the Ori has breached SGC and spread to the rest of Colorado.

Gerak proposes to the high council that the Religion of the Ori should be adopted by all Jaffa. Meanwhile, as Carter and Dr. Lee search for sound frequencies to make the Priors unable to access the highly evolved parts of their brains, a Prior disease threatens to contaminate the whole country.

A strange lab is found by SG-1 that was possibly used by Anubis. This lab contains an advanced human in cryo stasis. When taking him back to the SGC, the team and the rest of Stargate Command have to decide what to do with him.

A lone Jaffa is found dead after a hit and run on Earth, and trying to find out why he was here, Teal'c heads to Dakara to question Gerak. They find out that Ba'al is inf act on Earth in hiding. Now the SGC has to deal with finding Baal on Earth and trying to stop Gerak's Jaffa from running around Earth looking for him while running the risk of exposing the Stargate program, as well.

While trying to stop the Ori from getting a foothold in our galaxy, SG-1 loses a friend but gains an old one back.

Daniel comes face to face with the Ori, the beings posing as gods in this new galaxy and unknowingly reveals the existence of life in our own galaxy to them.Back at the SGC, the bodies of Daniel and Vala are still unconscious, but Dr. Lam reports that they are back to being stable again for now. General Landry meets with Gerak, who is now basically the leader of the Jaffa nation, to start work on an official treaty. This is interupted, however, by Mitchell and SG-12 bringing back a prior through the gate.Daniel and Vala manage to get back into their own bodies in the SGC for a short period, just in time to tell everyone about the Ori threat that is now heading towards our galaxy, but are then sucked back into the Ori galaxy.After hearing about the Ori threat, Mitchell confronts the Prior, who sends them a message about the power of his faith. After this, Daniel and Vala get taken by the villagers. Seeing that their heart rates are rising rapidly again, Mitchell must quickly find a way to get them back into their own bodies.

All of the original members of SG-1 have now left the SGC, and Lt. Col. Cameron Mitchell has now been given command of an empty SG-1, as a reward for the work he did in the battle over Antarctica (Episode 7x22). Mitchell tries in vain to get the original members of SG-1 back together, but none of the team seems to want to. That is until Vala Mal Doran, an old "friend" of Daniel's, comes through the gate with an interesting proposition.This leads the slightly smaller original SG-1 team, with Mitchell, in a new direction, away from the Goa'uld, and in search of more knowledge of the Ancients.