SG-1 manage to reassemble from their various desperate cliff-hanger perils, but the Ori are through the gate, wreaking havoc in the galaxy. Vala's daughter Adria is born, and matures at a great rate, becoming the spiritual leader of the Ori.
Searching for clues to Merlin's weapon, the team find a planet where all the local inhabitants have just laid down and died. The team catch the sleeping disease themselves, and must race to find a cure. Meanwhile, Vala is trying to pass a psych evaluation to be allowed to join SG-1.
SG-1 go to Atlantis. Daniel Jackson is searching for the two lost planets where Merlin's weapon might be found, and encounters an Ascended being giving him covert information. The rest of the team attempt to shut down the Ori supergate with the help of some other gates and a black hole. They succeed, and also destroy on of the Ori ships in the process.
Ba'al gives himself up to SG-C, claiming he knows the location of Merlin's weapon. All he wants in exchange is the destruction of his numerous clones. SG-1 suspect a trap, but play along with Ba'al. But when all the clones are captured and held in SG-C, they escape, and force Carter to give them the database of thousands of planets that might hold the key to the location of the weapon.
SG-1 are invited to join the General for a relaxing week-end in the cabin. Only Mitchell gets there before a crisis erupts: savage beasts are killing villagers on two planets recently reconnoitred by SG teams. Carter, temporarily in charge of SG-C, deduces it has something to do with the new Sodan shield technology. And a Gou'ald agent spying on the General using a stolen shield inadvertently causes beasts in the surrounding forest to become infected.
In the 200th episode, SG-1 have to help out Marty the producer [ 5.12. Wormhole X-treme! ] with a movie plot, as "plausible deniability" cover for SG-C. An absolutely hilarious set of meta-self-referential scenes ensue.
The Jaffa unleash the Ancient replicator-destroying weapon, modified for organic life, on an Ori-conquered world. SG-1 witness the event, as does Adria. SG-C protest the genocide to the Jaffa, but they spurn the alliance with Earth, saying this weapon is their only hope against the Ori. Adria discovers the Jaffa were responsible, and destroys Dakara in return.
A Goa'uld kidnaps Vala, wanting the memories of her ex-host. During a rescue bid, the device malfunctions, causing Vala to lose her memory. She wanders off, with both the Goa'uld and SG1 searching for her.
The Odyssey is space-jacked by the Lucian Alliance. It is badly damaged, and a captured Carter is forced to repair it, after Colonel Emerson is murdered in front of her. Meanwhile, the rest of SG-1 are trying to track it down, but Daniel and Vala themselves are captured. Mitchell goes undercover to effect a rescue.
Vala dreams of how to find the gate address of Merlin's planet, and SG-1 go to investigate. They find the Jaffa there a few days ahead of them, then the Ori arrive. After traversing several challenges, and picking up Ba'al and Adria on the way, they finally find a hologram of the Sangraal, only to be attacked by a dragon...
... they defeat the dragon, then find Merlin in stasis. A defence mechanism gates them all, except Adria, to an unknown planet, where Merlin attempts to recreate the weapon. He dies, but not before downloading his knowledge into Daniel Jackson, who starts constructing the weapon. Adria finally catches up with them, and in the final firefight, Ba'al is shot, SG-1 escape through the gate, all except for Daniel, who is captured by Adria, who wants Merlin's knowledge from him.
SG-1 take Merlin's dimension shifting device [ 9.18. Arthur's Mantle ] to a planet threatened by the Ori. They plan to use it to hide the village, but the power fails just as the Ori arrive. In the battle, Carter is seriously injured, but manages to tell Mitchell how to activate the shield over the room they are in. Vala is taken to the Ori ship, to be taught the Ori way, by Tomin, her husband from the Ori galaxy. The Prior discovers the existence of the shielding device, and decides to destroy the entire village, despite the fact that most have now agreed to follow the Ori. Tomin argues with him, but is overruled. Carter, despite being high on morphine, manages to get the device working again just in time. Tomin frees Vala, who sees devastated land, then the village reappears around her.
While experimenting with extending the range of Merlin's dephasing device, Carter is accidentally transferred to a parallel universe, where the US is under martial law after the Stargate programme was exposed. The Ori are about to attack parallel-Earth, and Carter uses the device to shield the earth from attack. The establishment decide that she is too valuable, both as a scientist and hero-figure, to let her return to her own world. But once she starts speaking publicly in favour of democracy, they decide she should return.
Daniel Jackson reappears, as an Ori Prior. SG-1 capture him, and he tells them he has been faking, and has a plan to destroy the Ori. However, as this plan requires him finishing Merlin's weapon, which could destroy the Ancients, and unblocking the wormhole, which could allow the Ori back in the galaxy, SG-C is dubious about believing him. SG-1 go to carry out the plan instead. The completed weapon is sent through the unblocked wormhole, but no-one knows if it worked. Four new Ori ships come through. Jackson is returned to normal.
After SG-1 blow up several of their cargo ships, the Lucian Alliance put a bounty on their heads. The team is spread out -- Carter at a weapons conference, Mitchell and Vala at his High School reunion, Jackson in a research library, Teal'c with some Jaffa -- as the bounty hunters track them down, and tangle with each other.
SG-1 discover that a ring on an alien planet is not in a tomb, but in a museum. They are mistaken for terrorist rebels, and end up holding museum visitors hostage. They can't dial out, and need to stall for six hours until SGC makes contact. But the hostage negotiators are uncompromising...
A rogue Jaffa, Arkad, attacks a Jaffa leadership conclave, killing many, and gravely injuring both Teal'c and Bra'tak. Teal'c goes undercover to kill him, both for this outrage, and for previously arranging the murder of Teal'c's mother. However, Arkad contacts SGC and tells them that he will help them stop a planned Jaffa attack on Earth. So the rest of SG-1 are ordered to stop Teal'c. They fail.
Vala's con-man father turns up with information about Arkad's plan. He helps SG-1 track down a naquada-powered fleet and destroy it, in return for sanctuary on Earth. But this is just part of a scam to get hold of some naquada himself. SG-1 out-scams him in the end.
SG-1 hatch a plot to capture Adria, but Ba'al steals her away at the last minute, and implant the Ba'al symbiote in her. Ba'al in Adria claims that all the Ori have been killed. SG-1 enlist the help of the Tok'ra to remove the symbiote, but it flushes a deadly toxin into Adria before it dies. Realising she is dying, Adria Ascends.
The Asgard are dying, so give Earth all their technology, installed on Odyssey. But this enables the Ori to track them. Carter has to shield them in a time-dilation field to save them, and it takes 50 years before she figures out how to get them out again...