Colonel Mitchell is given command of SG-1, after his heroism in helping to defeat Anubis' invasion [7.22 The Lost City]. But when he arrives, he discovers that Carter has left, to head the R&D team, Daniel is leaving, to go on the Daedelus, and Teal'c is engaged in the Jaffa elections, trying to stop Gerak becoming leader. He is told to pick a new team. Then Vala arrives, with tales of a great treasure, and traps Daniel into helping her with an Ancient wrist band that binds them together. Daniel realises that Merlin was an Ancient, and they all go to Arthur's tomb to search for Avalon. Underground, out of contact, trapped, they have to pass some tests before the ceiling descends and crushes them all...
... they pass the tests, which lets Colonel Mitchell draw the sword from the stone, then fight a holographic knight. Once they have passed the final test, the treasure appears. In includes a book about where the Ancients originated, and an Ancient communication device. Back at Stargate Command, they investigate the device. Daniel and Vala activate it, and find themselves transported into the bodies of two people on a strange medieval world, leaving their unconscious bodies behind them. The locals are forced to worship the Ori who claim to have created them, and have strange powers, but some have evidence of an older origin. When Vala blasphemes, she is burnt to death as a heretic. Back in Stargate Command, her body dies. But then in the village a strange being appears, and resurrects her burnt body, and commands Daniel and Vala to follow him...
...Vala and Daniel are taken to the place of the Ori, ascended beings who demand all should worship them. Through Daniel, the Ori have discovered a whole galaxy of Unbelievers. The ascended Ancients have stopped the Ori interfering directly, but the Ori followers have sufficient miraculous powers to convert many, and the Ori can send them through stargates. Their followers plan a holy war.
Vala releases the wristbands, but she and Daniel are still bound. They engage on a difficult quest to discover how to remove the bond, only to discover that it "may wear off in time". Meanwhile, a Senate Committee is set on slashing the Stargate budget, and the only way to avoid it is to get international funding, and international oversight.
There have been many reports of Ori Priors on Stargate worlds, including one where Vala's previous Goa'uld parasite reigned as a god. The team go there, and Vala is recognised as a god. They discover the Ori Prior healed a dying man, and is due back soon. When Vala confesses to being an imposter (at Daniel's insistence) she is put on trial. During the trial, the Ori Prior returns, and Daniel challenges him. People start getting sick, including Mitchell. Vala uses an Ancient device to cure them, but they sicken too fast, and re-sicken, and one dies. A Stargate medical team goes to help, but to no avail. The Prior returns, and Vala tries to gun him down, but the bullets stop without hitting him. He cures all the sick, including resurrecting the dead man. They all turn to the Ori.
A Prior sets a forcefield up around the Stargate on a Jaffa world. A minor Goa'uld comes to warn SG-Command that this is dangerous, and they should attack it with everything they have. Sam Carter comes to help, and they take the Prometheus to the planet, and bomb the forcefield with the biggest naquuada nuke they have. It merely uses the energy to grow, and they realise they have been duped. Once the forcefield covers the entire planet, it starts building an enormous Stargate, and compressing the planet to a black hole to power it. Vala destroys the invasion Stargate in a stolen ship, but when she tries to ring back to Prometheus, her matter stream is sucked into the black hole back to the Ori galaxy.
Gerak's Jaffa are discovered on Earth, searching for Ba'al. Ba'al threatens to blow up a naquaada bomb unless he is left in peace. SG-C discover where he is hiding, and plan to launch a cruise missile. But Ba'al discovers their plan, so declares a skyscraper in Seattle will be blown up. It is evacuated, and Carter discovers the bomb is embedded in the very fabric of the building. Mitchell gets the Prometheus to beam the whole building into space. The Jaffa invade the base, and SG-C launch the cruise missile. The Jaffa capture Ba'al, and execute him. But SG-1 discover a cloning facility -- there are now several Ba'als, still on Earth...
SG-1 search for the the legendary Jaffa warriors of Sodan, free of the Goa'uld for the last 5000 years. They are ambushed, and Mitchell and a Sodan warrior fight, and nearly kill each other. Mitchell is captured by the Sodan, and SG-1 capture the injured Sodan warrior. Mitchell is healed, then forced to train for a ritual battle of vengeance for shedding Sodan blood. He discovers that an Ori Prior is also visiting the Sodan, who are turning to the Ori, from the Ancients who they have been worshipping. He can't convince the leader of the danger, but does convince his trainer, who arranges his escape. Meanwhile, SG-1 are trying to convince their captive of the danger of the Ori, with little success. When Mitchell returns to them, they send the warrior back, with warnings.
SG-1 find a man in stasis, apparently having been experimented on by the Ancients. They bring him back to SG- Command, where he appears bewildered, and asks to be sent home. But Daniel discovers that he is in fact Khalek, a being created by Apophis, with some of his memories and characteristics, being trained for ascension. He must be removed from Earth before he reaches his full powers -- but the newly imposed Oversight Committee wants to study him.
Sam tries to build a machine to suppress the Prior's powers, based on what was learned from studying Khalek [9.09. Prototype]. SG-6 inadvertently bring the Ori plague [9.05. The Powers that Be] back to Earth, where it spreads like wildfire. Orlin, an Ancient previously known to Carter [5.03. Ascension], now de-ascended to a young boy's body, appears to help them find an antidote -- they need the infecting Prior's DNA to do so. He also says that the Ori want followers because they drain their power, and don't ascend anyone, not even the Priors. Meanwhile, Garak has been seduced by the Priors, and is calling for all Jaffa to follow the Ori. He has a crisis of faith when asked to kill Jaffa, and the Ori reveal themselves, and make him a Prior...
Mitchell and Daniel return to the planet of the Sodan [9.08. Babylon] to try to use Sam's device to capture the infecting Prior. They find the Sodan disenchanted by the Ori, and willing to help. Meanwhile, the plague continues to spread. Teal'c is opposing Garak's move to force all Jaffa to follow the Ori, by threatening civil war. Sam's device works, and they capture the Prior, and take a blood sample. But Orlin's powers are fading fast, and he is unable to make a cure for the plague. He goes to try to turn the captured Prior, who lets it be known that the Ori's real purpose is to destroy the Ancients. Meanwhile, Teal'c manages to turn Garak, who returns to Earth, and cures the sick at SG-Command, being consumed by fire as punishment. Dr Lam the uses this to develop a vaccine for the rest of the planet. Orlin is left brain-damaged, with no memory of Sam.
On a planet that has adapted Goa'uld memory-altering technology, Mitchell confesses to the murder of a senior scientist, because he remembers committing it. The planetary emissary is willing to grant him diplomatic immunity, but he insists on a full investigation, to find out if his memories have been altered, and by who. Eventually, the estranged husband of the victim is revealed, but he merely has his memories of the incident wiped, because he is important to the memory technology project..
A strange ripple in the spacetime contuinuum transports various SG-1 teams from parallel universes into SG-Command. Sam discovers it's due to the wormhole passing near a black hole. It looks like the only way to shut it down is to destroy the link -- but that would strand all the teams. They set out in Prometheus with the first of the parallel teams to come through -- who hijack the ship to steal the Atlantis ZPM for their own world. Sam realises this means they know how to get back. This team out-think the hijackers, return home, and send all the teams back.
The Jaffa council are being brainwashed into rejecting calls for democracy. Then Teal'c is kidnapped, but resists the brainwashing. Ba'al is behind it -- he claims he wants the help of the Jaffa to fight the Ori. The rest of SG-1 mount a rescue mission, and scupper Ba'al's plan.
A fugitive from the planet where SG-1 sparked a religious civil war [8.05. Icon] comes to them for help: a Prior has shown one side how to build a devastating weapon that will annihilate the other. He brings schematics of the satellite, and Sam says it can easily be destroyed by Propmetheus. Daniel goes back through the Stargate, to negotiate, but is arrested for treason. The Prometheus goes to destroy the satellite, but discovers it now has a shield, and the Prometheus is destroyed. The survivors help the other side create a missile to stop the base communicating with the satellite, so that it can be destroyed. Daniel negotiates a last-minute truce, and the team return home. But after they leave, talks break down ...
SG-1 are captured by Alliance bandits when their Stargate is beamed away, foiling their escape. The bandits blame them for stealing the gate, and are just about to execute them when Odyssey beams them to safety. They learn that Ba'al is stealing the gates to set up a new empire. They track Ba'al's ship, and steal the gates back. just as the Alliance arrives and destroys Ba'al's ship.
SG-1 are given "babysitting duty", escorting a committee to tour the Gamma site. But while there, a genetically engineered carnivorous bug escapes, and starts multiplying exponentially, destroying the main base. The team and the diplomats must stay alive long enough to await rescue by the Odyssey, but the bugs are voracious... [fortunately, there are sufficient redshirts to be eaten along the way]
As a result of Sam's messing about with Merlin's computer, she and Mitchell get "dephased": pushed into an alternate dimension. Meanwhile Teal'c goes off to the world of the Sodan, to answer a distress call. He discovers them nearly all slain, by one of their own kind infected by a Prior. He and his team are trapped, and dephased Mitchell accompanies the extraction team. Dr Lee, in his fiddling, manages to dephase Daniel, too. Daniel realises Merlin invented the dephaser to keep his researches secret from other ascended beings: a weapon to kill the Ori. Mitchell discovers that Teal'c can see him when wearing a Sodan cloak. They plan how to kill the rogue Sodan warrior, using Mitchell's invulnerability. Back at SGC, Daniel manages to dephase everyone -- just as Mitchell is engaged in a fight with the Sodan. Teal'c intervenes, and they defeat the infected warrior.
Vala contacts SGC from the Ori galaxy, through Daniel's body, to warn of an impending massive Ori invasion. The Russian's claim they want their Stargate back, but really only want a Prometheus-class ship. SG-1 get permission to check out the planet where Merlin claimed to have hidden his Ori weapon.
SG-1 arrive in Camelot, but find Merlin's library guarded by a Black Knight. The Ori's new supergate is found, and Sam and Teal'c go off to help, while Daniel and Mitchell stay to search for the Ori weapon. Sam tries to modify the gate to allow them to dial out, but the Ori dial in before she can complete it, leaving her floating in space. The Ori ship arrive, and start blasting the defence fleet. Vala goes into labour...