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.

Using an Ancient communication device, Daniel and Vala are transported into the bodies of two villagers in a distant galaxy. Once there though, Daniel and Vala find that there are beings posing as gods which are much worse than the Goa'uld ever were. Meanwhile on Dakara things are not going well for the new Jaffa nation. A lot of the Jaffa cannot understand why Teal'c is still spending so much time with the Tau'ri even though he says that finding out about the Ancients will be a great help to the Jaffa. Back in the other galaxy, Daniel and Vala run into some trouble which leads to a big problem for Vala.

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.

Vala and Daniel, still feeling the effects of the bracelets even after they have been taken off, cannot stray too far away from each other. Vala tells them that they have to go find the scientist that she stole the bracelets from to find out how to reverse the effects. This turns into a trek around the galaxy, trying to find the solution.

Vala learns that one of the planets she ruled as a Goa'uld has been visited by an Ori Prior and convinces SG-1 to try and go there to convince the inhabitants to refuse the Prior's offer. As usual, all is not as it seems with Vala's being there until the Prior visits again and unleashes a deadly plague.

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

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.

When Teal'c leads the team to find a secretive Jaffe sect known as the Sodan warriors, they are attacked and get split up. Mitchell is attacked by one of the Sodan warriors, but is able to mortally wound him, however, being hurt, then loses consciousness. He is then taken by the Sodan to be revived and fight in a battle to the passing against another Sodan warrior, to revenge the passing of one of their brethren.

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.

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.

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. Stargate Command's work is hindered by several of Earth's representatives assigning blame to the SGC for the plague; and then there's Gerak's previous conversion to a Prior, and his using his voice among the wavering Jaffa.

While visiting a planet inhabited by a potential ally, Mitchell wakens to find he is been accused of cuddle. Worse, he has awoken in the dead woman's abode. Mitchell also has memories of hugging the woman, too. SG-1 believes the memories are false, and have been implanted by an experimental device created by the scientists there. Not only do they need to prove the memories were implanted, but also who did it and whohuged the woman Mitchell is accused of cuddleing.

The SGC receives an IDC from SG-1, but it's before they are suppose to be back. The team arrives, and then another duplicate SG-1 team arrives, this time, on time. Then several more duplicate SG-1 teams arrives. Carter believes the duplicate teams are from parallel universes. However, one of the duplicate teams seems to have an ulterior motive and a plan. A plan that puts the real SG-1 team in eminent danger.

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.

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.

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.

Representatives from various countries who want to know more about the Stargate and the SGC are taken on a visit to the Gamma site. Unfortunately, at the same time the Gamma site scientists are investigating strange bugs from another planet, believed to be part of an Ori plan to scare worlds into worshiping them. The scientific study leads to the imperilment of the representatives and the Gamma site, as the bugs get out of control. SG-1, having been especially assigned to protect the representatives, must find a way to get them safely back to Earth, before they are consumed by the now carnivorous Ori bugs.

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 hugging 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.

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.

SG-1 travels to planet with the gate address found in the episode 'Arthur's Mantle' to find the Anti-Ori weapon. There they discover a pre-industrial village. In the Camelot town square, as the town is known by on the planet, they find a sword in a stone. Upon talking to the villagers, they learn that Merlin had a library or sanctuary in the town, too. The problem is the curse on the library. Anyone entering the library winds up dead at the hands of the Black Knight defense mechanism. Mitchell will have to fight another Knight in order for them to gain entrance. The search for the weapon is interrupted by news that a new Ori super gate has been detected. The teams split in to two's with Jackson and Mitchell returning to search for the weapon, and Carter and Teal'c joining the Odyssey, which is on its way with all the ships that can be mustered, to try to destroy it. Can the super gate be destroyed in time? If not, can Merlin's weapon be found in time, if the Ori do make it through the super gate before it is destroyed?