The Tok'ra send Jacob Carter/Selmac to the base and ask for help finding Seth, an ex-Systemlord Goua'uld that they believe have been hiding in Earth since the Egyptians buried the Stargate. He explains that Seth is hiding from the other Systemlords since he tried to overtake Ra.
Selmac tells Captain Carter he requested the mission because her father, Jacob has an unresolved issue with her brother and it is irritating Selmac. She says he doesn't talk to her either, but she has his phone number.
Meanwhile Daniel, Teal'c and Colonel O'Neil manage to track down a possible suspect of being the host of Seth. His name is Seth Fargough, and he is the leader of an extreme cult. He has around fifty followers and according to the classified documents from the USA government he can heal and make his eyes glow.
The SG1 team plus Jacob/Selmac travel to the location where Seth has barricaded himself with his followers. There they meet a guy who's been trying to recover his son from there. He asks them to rescue his boy and offers help. O'Neil and his team make a reconnaissance trip to the cult base and establish there really is a goua'uld present, the followers are heavily armed and have zats too.
Jacob says that Seth must be using Nishta to make all his followers do whatever he wants them to, like the one Hathor used on the SGC a while before, but stronger. He says that the Nishta has a weakness, once it have been reversed, the person infected gets immune, and the way to reverse it is by zatting anyone infected, but only after the Nishta has taken all the tissues, otherwise it will mutate and become immune to the zat gun.
The President calls the ATF and orders them to step down, putting Col. O'Neil in charge of the operation. O'Neil puts all ATF personnel in search teams looking for tunnels that lead to the cult's main building. Teal'c finds an entrance to the tunnels.
Capt. Carter has an idea that O'Neil, Daniel and she should go inside, since Selmac and Teal'c would be easily detected. They create a listening device that can zap them out after the Nishta infects them completely, so Teal'c and Jacob/Selmac stay in the camp listening to everything to zap them in the correct moment.
They go into the tunnels and are quickly caught. Seth infects them with the Nishta and asks them who they are and what are they doing there. He senses Samantha was once a host and wants to know more, she tells him it was a tok'ra. At that moment Teal'c zats them before they can tell Seth anything that can harm their plan. Seth orders one of his followers to kill them, but once they're alone with the guy, they zat him.
Meanwhile Seth orders everyone to distribute explosive devices throughout the complex. Tommy comes to it and they discover it is the son of the man they met earlier. He helps them to find more zat-guns and together they start zatting and transporting all the people out of there. Seth catches O'Neil and Teal'c sending the last few people and disables them. He disguises himself as one of the cult followers and goes out through the tunnel.
Teal'c and O'Neil are able to get out just as the explosives go off, and manage to warn Carter and Selmac about Seth. Selmac puts on a hand device an goes looking for Seth amongst the people in the tunnel, but Seth is quicker and uses his hand device first on Selmac. He gives his device to Samantha and tells her she cannot let him escape. She finds and kills him.
After all is finished, Jacob and Sam go to visit her estranged brother to patch things up.