Mitchell must attempt to rescue Carter, who is still stuck in space with ever-diminishing means to survive. Vala gives birth to a daughter and names her Adria, but the baby soon begins to age exponentially. Meanwhile, the Ori's hostile takeover of Chulak continues.
The SG-1 tries to locate a weapon, discovered to be in existence by Daniel, that could help stop the Ori's increasing threat. The team soon, however, finds itself at the mercy of a virus that induces a permanent sleep.
The SG-1 team heads to Atlantis to try and figure out how to stop the Ori, including a look into the vast knowledge base of Merlin with regards to a weapon he designed to combat them.
Ba'al's ship is shot down and lands on Earth in the midst of the SG-1 command's continued attempts to find a weapon that can destroy the Ori. Ba'al seeks assistance in destroying his clones gone rogue and, as payment, claims to be able to impart the location of the weapon SG-1 seeks.
As Landry and Mitchell await their SG-1 team members on a retreat at General O'Neill's cabin, Teal'c takes on a mission with SG-3 and learns that an alien beast is responsible for mass killings on another world.
As the team prepares for its 200th mission in the off-world, film director Martin Lloyd comes to the SGC looking for help with his next feature film script. Though the team is less than enamored of the idea of helping him, the Pentagon believes that Martin's film would help keep the Stargate program a secret to the public.
Vala's half-Ori daughter, Adria, has grown up and, as an Ori military leader, arrived to recruit soldiers into her army. SG-1 is forced to deal with her acquired methods of brutality while confronting the Jaffa.
Vala is ambushed, drugged and kidnapped from a fancy restaurant. Vala finds herself captured by the Trust. The Trust attempts to retrieve Vala's repressed memories to find its way to a secret treasure.
Odyssey is attacked by Lucian Alliance Members. Cameron Mitchell goes undercover to infiltrate Lucian Alliance to avert a probable alliance civil war.
The SG-1 team continues their quest for the Holy Grail, an Ancient device capable of killing the ascended Ori. They learn that an old nemesis is also looking for the device.
The SG-1 team finds the Ancient Merlin who can build the weapon that will destroy the ascended Ori. But he dies before he can complete the weapon's construction, so it's up to Daniel -- who has gained Merlin's total knowledge thanks to a magical object -- to complete the weapon before Adria finds them.
Carter tries to use the Merlin's technology to stave off the Ori's approach on a planet threatened by the unceasing force. The Stargate determines that their best bet in eventually defeating the Ori is making a stand now.
Carter gets sucked into a parallel universe where the Stargate team has been broken up, Atlantis has yet to be discovered and on Earth, martial law has been declared following the revelation of the Stargate program.
The Stargate team captures Daniel and find that he's been transformed into an Ori Prior. During their interrogation of him, he reveals that he has been faking his allegiance with the Ori and knows how to bring them down once and for all. But when the plan is put into action, it seems as though he's helped deliver the entire galaxy into the hands of its mortal enemy.
The Lucian Alliance puts a bounty on the heads of each Stargate team member after they deliver another damaging blow to their cause. Meanwhile, Mitchell attends his high school reunion and takes Vala as his "date."
The team follows Daniel's lead they hope will help them track down a bad guy, but their search takes them to a planet where they are believed to be rebels. Rather than fight their way out of the situation, the team quickly realizes they must play along and be rebel kidnappers if they are to ever get off the planet.
Teal'c hunts the people responsible for bombing a Jaffa peace summit, killing many and seriously injuring Bra'tac.
The Stargate Team meets Vala's father, a scam artist who claims to have information vital to the security of Earth. Meanwhile, Landry tries to reconcile with his ex-wife.
The Stargate team dangles Vala as bait to capture Adria and end the Ori threat, but Ba'al uses the confusion to take control of Adria and, as a result, the Ori army.