General Hammond leads a daring rescue attempt with the help of Teal'c to retrieve SG-1. Meanwhile, on board the Goa'uld ship, one of the members of the team gets a present from Hathor... is it too late to save Colonel O'Neill?

Jacob Carter/Selmak comes to Earth and tells SG-1 that a Goa'uld named Seth is hiding on Earth. Jackson tracks down several cults involving Seth to Washington state; however, the ATF also has an interest in stopping the cult leader. Furthermore, Carter, Jackson, and O'Neill are brainwashed.

Jack O'Neill is beamed to a ship. There he meets The Asgard high commander: Thor. Thor tells him that the Goa'uld are mad at the humans and are planning to attack Earth. The only way to prevent that is to include Earth in the protected planets treaty that the Asgard have with the Goa'uld. Jack has been chosen to represent Earth in the negotiations.

Daniel starts going crazy after SG-1 visits a planet where SG-1 found nine dead Goa'uld. The doctors believe he is suffering from the effects of traveling through the gate

The SG-1 team gates to the planet Orban to learn about their culture and their technology. The team decides to invite two Orbanians back to Earth, while two of the team, Jackson and Teal'c, remain to observe things there. Once back on Earth, the SGC is surprised to learn the Orbanian pair they brought back are not what they appear. The little girl, Merrin, is the one that has the technical knowledge the SGC is looking for, and the grown man, Kalan, turns out to just be her chaperone. This strange twist leads the team to investigate further, leading the team to propose drastic action to resolve the situation they find on Orban.

An alternate reality Carter and Kawalsky appear at the super secret Area 51 site. They say they have traveled through the Quantum Mirror. They tell the SGC that the Goa'uld are attacking the Earth in their reality, and are about to finish decimating Earth and the SGC facility. To make matters worse, the Alternate Sam appears not to be able to survive in this reality. Her body begin suffering temporal distortions which will eventually lead to her death. This reality's SG-1 needs to help the other SG-1 team save their Earth from the Goa'uld attack.

The team are captured by a bounty hunter who plans to use them to capture a Goa'uld, but all is not as it seems.

On a visit to a new planet, SG-1 finds a woman chained to a stake in the middle of a seemingly deserted village. They free the woman, Mary, only to find she had been chained as an offering to a demon. When the demon appears, SG-1 recognizes the creature. The demon tells the villagers that if he does not receive five humans the next day, he will destroy the village. SG-1 then find themselves being made the replacement sacrifice, when the village elder returns and calls them , evil.

When SG-1 gates to a new planet, they are surprised to find another SG team under attach from Jaffa troops. SG-1 renders aid to the unknown SG team, only to find they are not really SG soldiers, but Jaffa learning how to imitate SG soldiers, and for the Jaffa counter force to learn how to fight the SG teams. These Jaffa were under the control of Apophis, who is now dead. Can the team, now held prisoner by these trainees, must convince these trainees that Apophis is both a false god and is now dead.

Daniel and the team visit Abydos, only to find Daniel's wife Sha're. Daniel first sees her during a fight to help the Abydonians. He heads to her in her tent, and finds she is still the Goa'uld Amaunet. She uses a hand device to affect his mind. Teal'c follows, and kills her as Daniel is about to be killed. This later affects Daniel, and he grows to hate what Teal'c did. He resigns from the SGC. But strangely, Jackson is also having vivid dreams of her. Things take a twist as these vivid dreams play out.

The SG-1 team travels to a planet where the inhabitants all appear to be suffering from amnesia. None of them seem to know who anyone else is. However, the group SG-1 meets tells them about a woman who is working on solving their peoples' mysterious amnesiatic state. However, upon working with this woman, the team uncovers a horrible, deep dark secret about her, and what has happened to the population of the planet.

The SG-1 team travel to Sokar's home planet, after being informed by the Tok'ra that Sam's father is being held prisoner. The planet has been transformed into a literal Hell, and as there is no Stargate on the planet, so the team go down in descent pods - minus Teal'c, who stays with Martouf in the ship. Sam, Jack and Daniel locate Jacob, but become trapped. Sam has Jolinar's Memories, and Jolinar escaped from there once, but Sam can not figure out how to get to those memories back in order for SG-1 to escape along with Jacob.

In this second part the SG-1 team learns that Sokar is bringing his ship into orbit around Netu and decide to carry out a cunning plan; launch a bomb into the core of Netu, which will not only destroy the planet, but also kill Sokar. The problem is that after the bomb is launched - leaving them 12 minutes to escape - they stumble across an old enemy... Apophis, just as they are about to escape. Can their plan work? But more importantly, can they escape?

Teal'c thinks the Stargate Command has been infiltrated by aliens after seeing Dr. Fraser talking to three rather bizarre looking aliens. His fears are confirmed and it is up to Teal'c to find the others and stop the aliens from taking over the entire Earth.

SG-1 are informed they are to take part in a Tollan trial on Tollana, the person on trial is O' Neill's friend, Skaara and his Goa'uld, Klorel. Will Skaara be given back his own body? and what does the approaching Goa'uld ship intend on doing?

In a comedy episode the SG-1 team are seeing a person only they can see, his name is Urgo. He wreaks havoc with his games and chattering, which sends SG-1 up the wall and makes General Hammond they may have lost it. Can SG-1 get rid of Urgo?

SG-1 visit a planet to see the rare meteor shower, however things turn bad forcing them leave along with the natives who will go - however a fair number stay and O' Neill gets trapped on the planet after a meteor hits the Stargate burying it - with the planet being too far away to reach by ship and no allies available to help, can SG-1 possible bring back O' Neill and take the natives back to their home?

O'Neill turns to the dark side in this episode, and decides to steal Tollan technology, after the Tollans again refuse to share their technology. After being forced to retire over the incident, Jack is approached by the secretive NID organization to, in effect, do what he was fired for. However, can Jack trust the NID, and does Jack have an arterial motive in his actions.

The team arrive on unexplored planet Bedrosia, where their arrival is soon detected by a group of soldiers who capture members of the squad, believing them to be spies.

Apophis battles with the team to find the Harsesis, a being that could prove the undoing of the Goa'uld should he fall into the wrong hands.

The SG-1 team discovers a huge pyramid that could fit all the pyramids on Earth inside it, and still have room to spare. Inside this gigantic structure they find a crystal skull siting on top of a pedestal. Daniel claims that his grandfather has also seen one of these skulls before, and claimed it was a teleporting device, and that they must investigate this find. After traveling to the planet, Daniel looks into the eyes of the skull, and is about to be transported away, when Teal'c, trying to help Daniel, zat's the skull, causing Daniel to disappear before them. SG-1's only hope to find out what happened to Daniel, is to find Daniel's Grandfather, who, they find out, is currently residing in a mental institution. Can Daniel's Grandfather help SG-1 save his grandson?

Thor snatches Jack in the middle of him asking Carter to join him on a fishing trip to Minnesota. Thor has snatched Jack as Thor's ship has been invaded by a new enemy, and Thor believes Jack, with his less developed way of thinking may be of help exterminating the infestation. However, Thor tells Jack it will most likely be a one way trip, with little chance of success. Things get worse as Jack realizes this new nemesis may pose a major threat to Earth, too, if he fails.