With the threat of the Ori now pressing upon the Milky Way, SG-1 continues its desperate search for any way to stand up to them. Still rumored but undiscovered is a powerful weapon invented by Merlin, who we have learned was a Lantian scientist (Myrdin, also known as Moros) who returned to Earth from Atlantis 10,000 years ago ("Avalon, Part 1, "Atlantis: Before I Sleep").
Merlin was once ascended, but chose to retake human form to create a weapon that can destroy ascended beings, in order to fight the Ori—and to keep that work hidden from the others of his kind, who have a strict rule of non-interference with unascended mortals ("Arthur's Mantle").
Continuing their search for the device, Daniel Jackson and Vala Mal Doran visit the Ancient city of Atlantis, now an Earth outpost in the Pegasus Galaxy. In the city's holographic room they discover Morgan le Fay, who is masquerading as the teaching computer's interface, a holographic projection of a 30 to 40-year-old woman. Along with Dr. Elizabeth Weir (Torri Higginson), they seek Morgan's help in discovering the whereabouts of Merlin's weapon—despite the fact that Merlin was apparently rebelling against the Lantians and the other Ancients in creating it.
Meanwhile, Carter, McKay, and Mitchell join the Odyssey for a dangerous mission. Having been unsuccessful in dialing out with the supergate the Ori used to invade the Milky Way galaxy, the team hopes to dial in from Pegasus since the supergate was designed to be dialed from another galaxy. Their plan is to plant a normal gate next to the supergate and another next to a black hole in the Pegasus. Due to relativistic effects of the black hole, once the two gates are connected they can virtually not be shut down. Then using a thermonuclear device, they will make the matter stream "jump" from the normal stargate to the supergate (the same plan that saved Earth in the season two episode "A Matter of Time.") Unfortunately, the first test is unsuccessful.
Compounding matters, Atlantis detects a Wraith hive-ship heading toward the Odyssey's position, but are unable to warn them due to interference from the black hole. They dial the SGC to have them to relay a message to Teal'c (who is positioned in a cloaked scout ship near the supergate) who can relay the message to SG-1.
Later, Daniel, Weir, and Vala are stunned to learn that Morgan is not a holographic interface at all: She is an ascended Lantian, the real Morgan Lafey, who is walking the line of breaking her vow of non-interference to help the humans battle the Ori.
She reveals to them that when the Lantians resettled to Earth many millennia ago, they found only a harsh land and primitive peoples. There was no hope to rebuild their great society, so they spread out, some seeding ancient civilizations, others living out their lives in secluded meditation. In this later fashion Morgan and Merlin both one day learned to ascend.
When he later descended to create the anti-Ori weapon, she was sent by the Others to watch him. Merlin was able to keep all his ascended knowledge when he retook human form and also many powers. Using these powers, he made the weapon.
Meanwhile, Doctor Mckay realizes that the problem isn't that they don't have enough power to make the matter stream transfer to the supergate, but that they can't sustain the thermonuclear reactions long enough for it to obtain the desired reaction. They decide to set off two devices, one moments after the first to get the necessary result. Unfortunately, this also fails, and now Teal'c is detecting an Ori ship heading toward the supergate, possibly to gather with others that are going to come through the gate. Carter tells him to extend his cloak around the gate on his end and wait it out. However, moments later he receives the message from the SGC about the Wraith about to prey upon Odyssey.
Back at Atlantis, Daniel and Weir argue that in Arthurian legend Merlin and Morgan were rivals. If she was sent to watch him and, if necessary, stop him, would she really be helping them to find the technology now? They realize that she is breaking the vow of non-interference just by talking to them and that she is a part of a small group of Ascended Ancients who feel that they need to get involved for their own sakes because the Ori will go after the Ancients after they conquer the Milky Way. However, this small group of Ascended Ancients are afraid of the consequences that will result from their interference.
The Odyssey, pulling out of the black hole, comes under attack by the Wraith, with their systems having been disrupted by the black hole. Carter theorizes that they can lure the hive ship into the black hole's pull and their systems should be affected too, including their jamming technology. Then the Odyssey can use the gravity well to slingshot away. The Wraith fall for the trap and as the Odyssey is flying away, they beam their last two thermonuclear devices aboard the hive ship. It explodes, right next to the open Stargate...
...suddenly, on Teal'c's end, the Stargate emits a blast of energy and then the matter stream jumps to the supergate, which dials and the Ori ship that had come to observe is destroyed in the unstable vortex of the forming wormhole. By destroying the Wraith hive ship, they not only sealed off the gate to more invading Ori ships, but destroyed one of them in the process. Even more amazing, the stargate on the Pegasus end was not destroyed, meaning they have the supergate blocked off indefinitely.
Meanwhile, Morgan is persuaded by Daniel to tell the group which planet they must go to and thus find Merlin's weapon. However, just as she begins to mention something important about the weapon ("Merlin's weapon is not..."), she is stopped at the last moment by the Others. After the confrontation, Daniel comes to the ugly realization that the SGC and their allies cannot expect any assistance from the Ancients.
