Sam is working on a relic found at the Glastonbury cavern when Mitchell tries to get her away. Sam gets a positive verification scan and she tries to stabilize it. There's a flash of light…and they vanish.
Sam and Mitchell are still in the lab and not only are okay, but Ancient lettering appears in the air above the relic. Dr. Lee enters the lab but doesn't see them, and walks right through them. They can touch each other but nothing else. Sam concludes something has happened to them similar to what happened to Daniel (in "Crystal Skull"). They try to contact Daniel as Sam figures he can see them but they're in a different alternate dimension and it's no luck.
They get a coded message through the Stargate on a non-coded sequence, and something hits the gate iris. Landry gets word Sam and Mitchell are missing and then they determine the message is from the Sodan. Going to the security tapes, they figure out what was involved when Sam and Mitchell disappeared. Teal'c and SG-12 teleport to the Sodan planet and see signs of energy fire. They find the village destroyed and corpses everywhere. Teal'c determines whoever killed the Sodan knew how to kill a Jaffa, and showed no mercy. They find Lord Haikon, whose symbiote is already dead.
Dr. Lee tries to figure out the Ancient device while they stabilize Haikon long enough to reveal that one person did it all – Volnek. He passes out and they get a call from the other SG team members. Teal'c and Major Hadden find one man dead and the other badly injured. They conclude Volnek is using Sodan cloaking, and find out he's sabotaged the teleport obelisk to let them get out.
When Daniel hears Dr. Lee mention stray lepton radiation, he connects it to the crystal skull and concludes it's related to the legend of Arthur's Mantle. Teal'c and Reynolds have no way to get to the Stargate and Teal'c takes a Sodan cloaking device to go after Volnek on his own and take him down.
Daniel figures out the device is a keyboard and can be accessed by those who are out of phase. They establish communications but Sam and Mitchell can't read the display and have to (very slowly) help Daniel translate. Out in the woods, Teal'c activates the cloaking device and starts tracking Volnek. While Sam works to translate the Ancient writing, Mitchell decides to go through the gate after they receive word Teal'c's team is out of contact.
Volnek, now a Prior, opens fire on Teal'c who manages to shoot him down. Lee figures out a way to possibly reverse the procedure, but Daniel is skeptical. He's even more skeptical when Lee goes ahead…and Daniel is shunted out of phase as well.
A lightly-wounded Teal'c returns and finds Haikon doing better. Haikon reveals that Volnek encountered a Prior who informed him that the Sodan had committed blasphemy and they were cursed. Volnek returned but after several days went berserk and killed most of the village. SG-22 and 23 arrive (with the cloaked Mitchell) and find out they're trapped as well.
Given access to the machine, Daniel determines the device was intended to keep Merlin's research secret…from his fellow Ascended. Sam figures Merlin must have given up Ascension to develop a weapon capable of destroying Ascended beings, including the Ori. Daniel does further research and finds the gate address where Merlin hid the weapon. Lee then tries to reverse the phasing process but runs into a bit of a problem. He tells Landry that he's depleted the energy source and they only have fifteen minutes until the phase transition is permanent.
The SG teams figure it will take several claymores to destroy the creature that was once Volnek, and Teal'c volunteers to do it despite the danger of being caught in the explosion. Teal'c (with Mitchell in tow) cloaks again at which point he can see Mitchell. Mitchell plans to lure Volnek out since he's still out of phase even thought he cloaked Volnek can see him. The plan goes off and Mitchell heads for the claymores with Volnek in pursuit.
Daniel works out a way to possibly get them back, but with Mitchell gone he may or may not revert with the rest of them. Daniel initiates the procedure at the same time Lee does, and they revert. Unfortunately, so does Mitchell…with Volnek closing in. The cloaked Volnek punches out Mitchell, but Teal'c moves in and shoots him down long enough for them to get clear before Volnek sets off the claymores. Mitchell manages to grab the crystal off of Volnek during the fight, and they're able to return for Earth in time for dinner.