SG-1 come across another SG team being attacked by Jaffa. They offer to help but are shot by the SG team members. When they awake, they find out that the other SG team are Jaffa, loyal to Apophis, who are planning to infiltrate Earth. Can SG-1 convince them that Apophis is dead before the Jaffa fight to the death?

Martouf leads a Tok'ra delegation with crushing news for Carter: her father Jacob/Selmak has been captured by Sokar and imprisoned on Netu, an Egyptian name for hell, on a moon of planet Delmal, where prisoners are sent to suffer eternal torture, and from where no one returns; only Jolinar has ever escaped. SG-1 mounts a rescue operation with Martouf, top-priority being any information Selmak can offer about Sokar's plan to subjugate the other system lords, an unprecedented threat for all humanoids in the galaxy. Teal'c must pilot a Goa'uld ship and keep it in orbit as landing is impossible except by small pod, but first Martouf taps into Jolinar's memory, which is partially blocked by some trauma beyond physical torture. Only when they're down and in the custody of Netu's lord Bynarr, does Sam realize he is the key, in a 'personal' way, but not voluntarily, as she had thought. Sokar learns of their presence from Bynarr and orders the team and craft destroyed, but this also means there must be a way out. Bynarr's prime, Na'onak, has, and is himself, a major surprise.

Now that Apophis has revealed himself, he promises the prisoners to overturn Sokar, which requires extracting an irresistibly valuable secret, to which end he drugs Sam with the truth serum 'blood of Sokar.' Apophis also implants a memory device in, and gives the drug to, Jack to torture him using the persona of his young son that died, and Daniel for the location of his Harsesis son. Martouf's love for Jolinar makes him betray that the Tok'ra are on planet Entac - a convincing lie, so Apophis's plan to earn Sokar's gratitude, and then kill him when rewarded with the lordship of Netu, is on a shaky basis. Teal'c must help the Tok'ra Aldwin prepare a nuclear weapon to explode the whole moon when his ship arrives as their last chance to eliminate Sokar, but he decides to rescue SG-1 instead, by flying in the path of the rings device on Sokar's ship when he arrives.

An alien incursion takes control of the base.

While on an archaeological dig at the original Goa'uld home world, Daniel is captured by a young Unas. He tries to communicate with it and slowly builds a rapport. Meanwhile, SG-1 comes to the planet to find Daniel and they soon realise that some of the SG-team members there may have been taken over by Goa'uld. Will they be able to discover which ones in time to rescue Daniel?

When SG-1 flees from an expedition with Col. O'Neill and some mysterious team member named Tyler, whom no one else knows about, stranded, the fitness of the team is questioned.

When Daniel's Unas friend, Chaka, is captured by another world's slavers, SG-1 goes to that world to rescue him.

The Russian SG team brings back a man who claims that his people are being experimented on by Nirrti. SG-1 investigate where the experiments are conducted, with the Russian SG team as backup. The inhabitants worship Nirrti as their god and savior from a terrible plague. SG-1 attempts to use the same device Nirrti used on the people to reverse the mutations, but the people turn on them at the arrival of Nirrti.

On a mission to observe a nebula, SG-1 finds a crashed ship and its three human survivors. They soon come under fire from an pair of aliens bearing the weapons of the survivors. They repel the attack, but one of the three is wounded. She is taken to the SGC for treatment while Sam attempts to repair the ship. Jack and Teal'c feel that there is more to the relationship between the aliens and these humans, and attempt to trap an alien.