The Jaffa Council are meeting and hearing a proposal from Brother Maz'rai to disband the Council to bring democracy to all Jaffa, but Sister Ka'lel speaks up against it much to Bra'tac and Teal'c's surprise. She had previously spoken privately in support and now they wonder what's going on. Maz'rai approaches Ka'lel in private and she zats him.
Mitchell is at a hospital making sure his friend Major Bryce Ferguson is receiving treatment, for an injury which took him out of the running of the SG program and from which he's now apparently dying. A guilty Mitchell is unable to tell Ferguson about the SG program due to his security clearance. The Jaffa Council is hearing Brother Maz'rai, who is now supporting the position he previously opposed. Maz'rai denies there is anything amiss and Bra'tac resolves to investigate the matter. While Mitchell meets with Ferguson, Bra'tac arrives at SGC to warn SG-1 that Teal'c has disappeared while seeking allies for their proposal, and he needs their help.
Teal'c wakes up to find himself a prisoner held by a Jaffa who inserts an implant into his temple. He then uses a hand-held device to inflict pain on him to "teach" him. Daniel and Sam vow to help while Mitchell takes some personal time to stay with Ferguson. They talk to Maz'rai who denies knowing anything and Bra'tac confronts him. Maz'rai admits that Teal'c was taken but doesn't know where. Bra'tac believes him and concludes that the man has been brainwashed. Meanwhile Ferguson tries to get some information on the Stargate project from Mitchell.
Teal'c interrogator U'kin meets with Ba'al and reveals Teal'c is resisting the procedure, so Ba'al goes to talk to him personally. Daniel and Bra'tac report to Landry about the brainwashing program, believing half the Council may be compromised. Bra'tac suggests that the Rite of M'al Sharran can break the brainwashing, as it once did for Teal'c against Apophis, and they decide to convince Maz'rai to undertake the Rite. Ba'al is chatting with Teal'c and pointing out they've worked together before and should work together against the Ori, with Ba'al leading the Jaffa.
Daniel and Bra'tac confront Maz'rai with the discrepancies between his former arguments and his current policy, and the fact he can't remember anything the night before his reversal. He asks them to leave and Bra'tac believes they've reached him and he will undergo the Rite upon consideration. Meanwhile Ferguson manages to come close to guessing what Mitchell is involved in but Mitchell can't confirm. Ferguson's doctor, Kelly, has the results of Ferguson's most recent test and confirms that he's dying from his head injury and there's nothing they can do without killing him even quicker. Mitchell then calls up Ferguson to ask a favor.
Maz'rai undergoes the Rite in private, and Bra'tac and Daniel find him dead. Daniel finds a piece of paper with Ka'lel's name on it. Ba'al asks Teal'c what his decision is but he remains defiant. Sam brings Mitchell up to speed on how they've found a mothership where they believe Teal'c is prisoner, and he prepares to head out. Ferguson reveals he's going to check out but Mitchell brings out the memory-sharing device from the Galarans ("Collateral Damage"). Mitchell hooks Ferguson up to share his memories of the last year with him then says he has to leave and apologizes for the fact he acted rashly, which is what got Ferguson injured. Ferguson says he understands and tells Mitchell to get going.
Teal'c is suffering from lack of tretonin, and is brought before Ba'al who taunts him with a vial of it before stepping out. Teal'c heads for the drug and injects himself rather then die as U'kin looks on, and then U'kin begins the brainwashing procedure again.
Landry prepares an assault team to go through with SG-1 leading the way to the planet where Teal'c is being held. They activate the Gate but it's a distraction as Bra'tac bombards Ba'al's troops from the sky. Then the assault team comes through with Bra'tac providing air cover before two fighters engage him. Mitchell, frustrated over the personal situation with Ferguson, goes charging ahead past the others as Bra'tac is shot down. A Jaffa attacks Mitchell, injuring him, but he knocks out his attacker and manages to take out the cannon that has the rest of the team pinned down. Mitchell then gets to the mothership where U'kin announces to Ba'al that Teal'c has been successfully brainwashed.
The mothership lifts off and Mitchell tries to board via the teleport rings. Ba'al wonders if Teal'c is faking and brings out a captured Bra'tac to test him. The Jaffa get the drop on Mitchell while Ba'al hands Teal'c a staff weapon and tells him to kill his mentor.
Daniel and Sam arrive to take out Mitchell's Jaffa and Sam beams Mitchell up while they cover for him against the retreating Jaffa. Mitchell goes charging through the ship while Bra'tac appeals to Teal'c who it becomes clear isn't brainwashed. Mitchell arrives and the three of them take out the Ba'al clone and his Jaffa guards. They teleport out just in time as the mothership goes to hyperspace.
Later Sam and Daniel wait to hear the news on the democracy referendum – Bra'tac and Teal'c emerge to announce now all Jaffa will be able to vote, and the brainwashed Councilmen will eventually prevail and recover. At the base Mitchell reads a letter from Ferguson, who has died in his absence, and Teal'c apologizes while thanking him for saving his life and Bra'tac's. Mitchell reassures him that there's nothing to thank – they watch each other's backs. And Teal'c reveals he resisted the brainwashing by knowing himself, something Mitchell considers.