Allegiance

Allegiance is the ninth episode of the sixth season of Stargate SG-1.

Plot
The Alpha Site prepares to receive several Tok'ra, who come through the Stargate fleeing an assault by Anubis' forces. The Tok'ra have suffered heavy losses and many are badly wounded or dead. One of them named Malek comments about the Jaffa on the base. One of the Tok'ra bring a Zatarc detector.

Later the dead Tok'ra are given a funeral ceremony where they are placed in front of the Stargate which is briefly activated and their bodies are vaporized by the kawoosh. However, during the ceremony a fight breaks out between a Jaffa and a Tok'ra, as one of the Jaffa had apparently insulted the ritual bringing a violent reaction by the Tok'ra. This sets an atmosphere of animosity between the Tok'ra and the Jaffa, as the Jaffa see the Tok'ra as no different to the Goa'uld and the Tok'ra have lost most of their number due to to Jaffa soldiers of the Goa'uld.

Later on Samantha Carter discovers that someone tried to sabotage a Naquadah reactor to overload and potentially destroy the entire site. They inform General Hammond on Earth about it and request that no-one is to enter or leave the site for fear that there may be a Goa'uld spy in their midst. The base is locked down, and they talk with the Tok'ra about the incident. They also start to use the Zatarc detector on the people on the base to find the saboteur, at first on the Tok'ra. They later go to check one of the Jaffa much to his disgust, but while they try to persuade him, a Tok'ra is found dead and one of them accuse the Jaffa who was quarrelling with the Tok'ra before. He is then examined by the detector and when it detects that he is lying, he is detained, although his prior feelings against the Tok'ra may have influenced the detector. They wait for the autopsy and it is revealed that the Tok'ra was killed quickly from behind, which Bra'tac concludes that it could not have been done by a Jaffa as they confront face to face. They then discover the accused Jaffa dead in his cell, perhaps killed by the same weapon. But this makes the tense situation between the Jaffa and Tok'ra worse.

When the dead body is brought away, a trade of insults between a Jaffa and Tok'ra escalates into all the Jaffa and Tok'ra holding their weapons against each other. As Jack O'Neill tries to calm the situation, Bra'tac finds footprints of an unknown person leading away from the camp, further suggesting a spy. The personnel are all accounted for and they follow the footsteps into the forest in groups of three, a Tok'ra, Jaffa and Tau'ri. After some time Teal'c finds a group dead and informs O'Neill. Bra'tac and Malek are then attacked and Bra'tac futilely tries to fight the invisible assailant. He is supposedly killed and pulled away. Malek flees and informs O'Neill that Bra'tac is dead. However Teal'c is enraged and nearly strangles Malek to death before he is calmed down. Malek informs the others about the invisible force and as they don't have any TERs available nor can they go through the Stargate to obtain one, they plan on using the Naquadah reactor to create a high-frequency electromagnetic field to attempt to de-cloak the enemy.

At the base all gather, while Malek and Carter prepare the Naquadah reactor for the field. They defend the Stargate, and speculate that the enemy is an Ash'rak - an elite Goa'uld assassin. While all the people wait for the field to be ready, the Ash'rak attacks and injures many of them, causing them to blindly fire their weapons, resulting in friendly fire. The Ash'rak escapes and one of the SG soldiers discovers that his GDO has been taken, further complicating matters.

Finally the EM field is ready and they can see the enemy. They attack but without success. While they prepare to reactivate the reactor the Ash'rak attacks again and then disappears. When the field is ready again, the Ash'rak prepares to attack but he is suddenly shot by a staff weapon, which turns out to be Bra'tac who is still alive, who reveals that he was left for dead in the forest. Malek shows his gratitude to Bra'tac for saving his life gives him his hand. In the end Bra'tac takes the Ash'rak's blade and comments how it did what they could not - bring them together against the common enemy.