Stargate Command is approached by representatives of Jonas Quinn's home planet seeking military hardware. Their world is divided into three territories and there is a long history of war among them. Jonas' country fears that the other two territories are about to sign a non-aggression pact thus making them vulnerable to attack. In return for arms, they are offering an abundance of Naquadria. SGC isn't about to get involved in what amounts to a civil war but there's another possible outcome when Jonas' one-time professor, Doctor Kieran, tells them of an underground movement ready to overthrow the government and seek out a lasting peace. SG-1 travels to Jonas Quinn's home planet to obtain information on the situation there but not all is as it seems.

Anubis's super weapon has been put out of commission, but Yu's fleet has been diverted to the other side of the galaxy by Yu himself, allowing Anubis to escape into hyperspace. Jonas has been captured by Anubis and Daniel is still aboard Anubis's ship, evading capture. Anubis uses the mind probe on Jonas, learns of Naquadria, and begins his attack on Kelowna. The Kelownans seek aid from the SGC. Jack and Sam arrive on Langara to discover that the Kelownans have given Anubis Naquadria in order to secure their safety. They communicate with Daniel who is attempting to free Jonas. Teal'c has convinced Yu's first prime to seek a new leader of the System Lords, Ba'al.

Using the Ancients' communication technology, Vala, who is in the Ori galaxy, contacts the SGC. She tells them that after being sucked into the wormhole she awoke in a bed in a village much like the one she and Daniel had visited when they used the communication stones. The locals think she fell from the sky - a gift from the gods - and befriends the gentle Tomin, a devout follower of the Ori who has a bad leg. Vala has two pieces of information for the SGC: first, she is pregnant though insists that she didn't have sex with anyone; and second, the Ori have been building a fleet of ships and building up its army. Meanwhile, Colonel Chekov advises General Landry that the Russians will not be renewing their working agreement with the United States and will be taking their Stargate.

As the Ori invasion continues, Vala and Daniel must deal with their leader, Vala's young daughter, who is rapidly aged by the Ori to serve their purposes.

During their quest for the Sangraal, SG-1 must join forces with their enemy and face a real-life dragon.

The SG-1 team hadn't counted on a real dragon as a guardian until one flies out, breathing fire. However, Daniel thinks the Sangraal probably is a hologram. They escape, but the dragon follows them outside. Ba'al admits not to know its secret name, while Daniel believes that the name probably holds power over it. While they guess, Cam thinks of luring the dragon to blow it up, but the C4 barely impresses its digestion. Daniel makes it disappear by using Morgan le Fay's name in Ancient, Ganos Lal. They find it had guarded the frozen 'grave' of the realm's arch-magician, Merlin (or rather, Myrrdin). Vala accidentally triggers a mechanism which revives Merlin when she approaches an Ancient repository device. In the meantime, the team is transported to another planet via the obelisk by the gate outside. Sam surmises that the gate and obelisk are programmed to dial automatically every few hours and transport them to a set of planets that are cut off from the rest of the gate system. Unfortunately, they can't dial out to any other planets either while the program is operating. When he comes to, Merlin seems to confuse the team and Ba'al, with Arthurian characters, but once convinced they are on the same side, he goes to work with the Ancient device to create the Sangraal. Merlin dies at the device, wishing them good luck and referring to one last task. Ba'al's stargate programming skills now seem their only chance. Daniel tries the Ancient repository device himself, but is knocked unconscious. Meanwhile, Adria keeps searching for them via the stargate dialing program on different planets- each time a bit quicker- being one planet behind them. While she is searching, the team is once again transported to another planet, minus Merlin's body. Daniel awakens with valuable memories from Merlin and tries to construct the Sangraal using the repository device again, in exhaustingly intense phases, and finds it also gives him telekinetic powers. It also messes with Daniel's mind, having two different personalities and memories present (his own and Merlin's). Before he can finish the work, Sam and Ba'al disengage the dialing device, just as Adria's Ori troops arrive, allowing SG-1 to escape. Adria is able to capture Daniel before he can escape as well.