Landry meets with SG-1 as they report in on the search for Merlin's weapon, and the fact the two gate addresses turned up blanks. While Daniel works at Camelot to decipher the texts in Merlin's library, they're interrupted by an arrival of a Goa'uld ship heading directly for Cheyenne Mountain. Landry orders the fighters to engage and they bring down the ship. SG-1 heads to the crash site where they find the pilot is… Ba'al.
SGC imprisons Ba'al and SG-1 wonders why he came in such an obvious manner. Sam picks up a signal and determines he has a locator beam on him, but SGC has jamming signals to prevent a teleport. Ba'al insists on only speaking to SG-1 and they agree, and he says his clones want him dead. Vala figures out Ba'al planned to wipe out most of the galaxy's populations to dissuade the Ori, but he didn't let the clones in on his plan and they turned on him. Ba'al offers them information on Merlin's weapon.
Agent Barrett arrives to take possession of Ba'al and says the Goa'uld infiltration of the Trust is a world-wide conspiracy, and Ba'al knows enough about them to break up the whole thing. However, Landry doesn't want to give up Ba'al. Ba'al tells them the gate address of the weapon is on the list downloaded into Jack's mind and he can narrow it down. Ba'al says the clones have locator signals in them and says it should be easy to destroy them. Landry is skeptical but feels they have no choice but to investigate, and he tells Barrett that he'll have to figure out what to tell his superiors.
They use the locator to pinpoint the Ba'al clones on various planets and then take the coordinates to the first one, with Vala along for her first mission. They find the ring teleportation system but Vala goes running off to find the activation controls against Mitchell's orders. Jaffa are on the planet and Vala takes out one of them and exchanges fire with another. They send for reinforcements by activating the ring and SG-1 departs as the Jaffa team arrives. Inside the base, SG-1 tosses in a grenade and disables the Jaffa, taking Ba'al prisoner. The clone claims he's the real Ba'al and he's the only one who knows where the weapon's location is.
They imprison the two Ba'als together and they fight each other until the guards stun them. The base scientists can't figure out a way to determine the real Ba'al. SG-1 goes to capture another Ba'al and Vala and Sam intercept one Ba'al while Teal'c and Mitchell capture the other. The various SG teams continue to bring in captured Ba'als while Barrett asks to have a few spares. Landry refuses and Barrett warns they'll get the President on board if Landry's plan doesn't work. They finally collect every Ba'al on the list and they try to bargain with the Ba'als, but they're not interested. Vala tries to vamp one of the Ba'als and convince him she plans to betray SGC. He calls her bluff and Barrett suggests his people can help.
When Landry still refuses, Barrett talks to Sam and tries to appeal to their friendship, losing his temper when Sam doesn't buy it. Barrett gets a guard to let him see one of the prisoners. Landry sees Barrett on the security monitor and then Ba'al overwhelms Barrett and takes his gun. Sam takes a soldier in while Ba'al takes out the cameras and makes his escape. Worse, Ba'al has freed the other Ba'als and uses stolen zat guns to knock out Sam and Barrett.
Dr. Lee works on releasing the symbiote poison to take out the Ba'als, but isn't sure if it will work on all of them quickly enough, so SG-1 goes to create a distraction but have to be in the proper position without being spotted. One of the Ba'als takes Sam to a computer where they're trying and failing to download the list of planets from the Ancients database. Teal'c's team almost gets spotted but they evade a Ba'al at the last moment.
Sam refuses to help Ba'al and he threatens to kill the other hostages if she doesn't cooperate, starting with Barrett. As Sgt. Siler rigs the vents, the Ba'als suspect that Sam is stalling but she eventually gets the database downloaded. A Ba'al reveals they have a different plan then escape and locks Sam up.
The Ba'als finally find the various SG teams and gunfire breaks out. Landry has no choice but to order them to distribute the gas as much as they can. Mitchell frees Sam who realizes what the Ba'als' plan is as they all retreat to one of the isolation rooms. SG-1 confronts the Ba'als as they all beam out to their backup ship in orbit then depart.
The team figures out that Ba'al's entire plan was to get captured then collect all the clones, each one having a locator signal that would cumulatively let them penetrate the jamming signal once they had the database. But SG-1 realizes that Ba'al couldn't have anticipated Barrett's involvement, and Sam and the others confront him over his interrogation of Ba'al and the fact Ba'al used mind control on the Jaffa Council. They point out that Ba'al has brainwashing tactics but Barrett denies any involvement. Landry takes Barrett prisoner and Sam blames herself, even though Landry reassures her that she did the right thing. Now they have to worry if Ba'al can get hold of the weapon.