A Jaffa is running through the woods on Earth in Virginia when he's hit by a car and killed. SG-C receives the file and Teal'c verifies he's a former Jaffa of Yu, now serving with Gerak. Sam is settling in when Daniel discusses the nearby factory belonging to Farrow-Marshall – their chief financial officer Alan Jameson is missing. Gerak is dealing with the Jaffa Council and advising caution in dealing with the Tok'ra when Teal'c and Mitchell arrive, and Teal'c points out they shouldn't be relying on force. Afterward Gerak denies any knowledge of the dead Jaffa and then leaves – Teal'c and Mitchell are sure he's lying.
Daniel goes to a diner near the Farrow-Marshall factory and meets with the financial officer's wife. She notes he was acting distant and "alien" for a few months. She hired an investigator who later quit, scared. Gerak goes to a secret chamber and confronts a silent prisoner who has resisted their interrogation – the missing Jameson. Sam meets with the company's rep, Charlotte Mayfield, and denies that anyone is involved with the Richmond factory. The rep also refuses to discuss what Jameson's business in Richmond was and has Sam "escorted" out of the facility. Afterward she meets with boss – Ba'al.
Daniel has been going through the files on Farrow-Marshall and turns up a pattern of disappearances, about the time the Osiris ship was destroyed. Daniel believes the Goa'uld who infiltrated the Trust are still on Earth. Mitchell and Teal'c are waiting for Gerak when one of the Jaffa councilors warn that Ba'al has been on Earth for nine months and the Jaffa was fleeing to join up with him. Teal'c advises they must find Ba'al so that Gerak can't capture him and use him for a propaganda victory to secure his power. Jameson breaks, revealing Ba'al's location, and the Jaffa land a ship on the factory on Earth. They're caught on camera and Ba'al's forces open fire while Mayfield and Ba'al head out.
SGC gets word of the attack and then Ba'al sends them a tape – he wants to be left alone by all of his former enemies and offers the following deal: SGC leave him alone or he'll detonate a naquadah bomb he's planted somewhere in the U.S. Scans come up empty and Sam suggests they use the symbiote body so they don't endanger his human servants. They head out and Mitchell has SG-1 patches for everyone now that they're back together as a team.
In orbit the Prometheus is scanning for the Naquadah and Mitchell and Teal'c head up to look for the Jaffa mothership. Daniel and Sam team up with Agent Barrett who has spotted Ba'al at a nearby hotel. Teal'c figures out that the Jaffa mothership is hiding behind the Moon and they take the Prometheus in and get a communication from the Jaffa warning them to stand down or they'll attack. On Earth they prepare to move in as Ba'al leaves the hotel, but Barrett orders them to stay away when Sam picks up Ba'al across town giving a live press conference about how he's expanding his businesses.
Teal'c tries to negotiate with the Jaffa commander to no effect, and prepares to tell the Council that Gerak has been lying to them. Gerak is already addressing the Council and is one step ahead of Teal'c – the Council questions Teal'c loyalty. Teal'c reads them the riot act about Gerak trespassing on Earth and gives them his word Ba'al will be brought before the Council. Teal'c and Mitchell return to Earth where SGC has a missile loaded with the symbiote poison and they're ready to fire. Ba'al is aware SGC is preparing to attack and he calls them up to tell them the bomb is in a tower at Seattle and set to go off. They have 45 minutes to find the bomb in the tower, which is being evacuated. While Daniel carries out the missile launch, Sam beams ahead to Seattle but they've been unable to pinpoint its exact location. As Ba'al clears out, the Jaffa arrive, while Sam figures out that the newly-constructed building is laced with naquadah.
They launch the missile (killing Gerak's Jaffa) and try to figure out how to deal with the building-bomb as they're out of time to evacuate enough of the area. Mitchell comes up with a plan – have the Prometheus beam the building into deep space. They succeed with seconds left, but Daniel reports that Ba'al has escaped. Teal'c meets with the Jaffa Council and Gerak reveals he has Ba'al as a prisoner. Ba'al gets in one last gloat before Gerak finishes him off for good. A disgusted Teal'c returns to Earth where they reveal that Ba'al has cloning technology and the one Gerak killed was most likely not the real one. Teal'c chooses not to inform the Council since they won't believe him – he realizes Gerak is calling the shots…for now. Several Ba'als are still alive, and all observing the televised cover-up with interest.