After losing Teal'c to Apophis, SG-1 and Jacob prepare to battle against their foe on board Cronus' ship. A mysterious ship appears which allows them to escape only slightly damaged. A later encounter with the enemy ship shows no signs of life on board, save for an army of replicator bugs and an auto destruct programme.

Teal'c, whose mind has been altered by system lord Apophis, now believes that the last four years he spent where working undercover for Apophis against the SG-1. The SG-1 need to find away to get his mind back. The team seek out Bra'tac, and ask his help. Bra'tac performs the Jaffa ritual known as the Rite of Mal'Sharran. However, this ritual will bring Teal'c to the edge of passing, by forcing him to relive events throughout his life.

While inspecting a mysterious weapon on a distant planet, Carter is inexplicably knocked unconscious. She is taken back to the SGC, leaving another team to investigate the aspects of the weapon. Carter finds that an ascended Ancient, Orlin, has followed her back to Earth. At first, she thinks he is imaginary, but then Orlin takes on a real human form to interact with her. He tells her testing the weapon will destroy the planet, and should not be tested. However, other forces now know of Orlin, and are watching Carter's every move. Things come to a head as Carter tries to stop the test firing of the weapon, and the secret governmental group's attempt to capture Orlin.

O' Neill stays behind on a planet with Lt. Tyler, a new addition to the team, as the others escape back to Earth. They ask to immediately return to the planet with, reinforcements to rescue O'Neill and Tyler, when Gen. Hammond informs them that there has never been a Lt. Tyler on their team, and that in fact, he does not even know a Lt. Tyler. Gen. Hammond denies the return, and forces SG-1 to be looked over in the infirmary. Col. Frank Simmons appears and begins his own investigation; only his motives appear to be more sinister. So, just who is it that O' Neill is helping, and can SG-1 on Earth convince the SGC to save O'Neill and the other entity before the Goa'uld capture orhug them?

SG-1 gates to a world which they find worships the Norse god, Freyr. The people believe the team are Elves, as disciples of Freyr are known as. All seems to go well until the planet's sky turns red. The local religious interpreter decries that the SG-1 team is the cause of this strange occurrence, suggesting that SG-1 has brought on Rag'norok on the people ? meaning the end of time. The events of SG-1's arrival lead to the possible demise of all of the planet's inhabitants, and the team's own peril. O'Neill is able to request help from the Asgard high counsel via their beaming viewing system in the villages temple, but the Asgard counsel tells him they are prevented from helping, due to provisions in the 'protected planets' treaty with the Goa'uld. SG-1 must find their own way to save the planet, and its people on their own.

When Cassandra exhibits strange uncontrollable electro magnetic effects, which cause most electrical sources nearby to burn out, she is taken back to the SGC. In investigating the cause, they are lead to believe Nirrti is involved in the strange development of children on Cassandra's planet. The team struggles to find the answer, or the cure, to Cassandra's situation. However, they get a nasty shock related to their investigation of Nirrti's seemingly abandoned lab on Cassandra's planet.

Daniel and the SG-1 team find Chaka has been captured by an agrarian society, which posses Goa'uld weapons. It seems the society uses the Unas' as beasts of burden. Daniel insists they try and rescue Chaka. Once on the planet, Jack and Daniel try to reason with the planet's Unas slave traders, while Teal'c and Carter keep watch from a nearby hill. Things don't go well, and the team decides to 'extract' Chaka by force. Unfortunately, this leads to Jack and Daniel being captured as well. It is then up to Teal'c and Carter to free them and Chaka. However, Chaka has plans of his own to take down his captors, and free his fellow imprisoned Unas, and Jack and Daniel, too.

On a rescue mission to recover Russian soldiers missing in action on a previously undisclosed trip, SG-1 get trapped in a Goa'uld tomb. Here they discover not only the remains of the Russian soldiers, but a hugger alien from which they must now escape.

SG-1 return to Tollana to discover the Tollans have reversed their policy on technology sharing and are now willing to trade advanced weaponry with Earth. But Carter's friend Narim warns that this spells great danger for Earth and the team must return to uncover the real agenda behind this reversal.

SG-1 finds a peaceful agrarian world upon a visit. The people there connect SG-1 with an amazingly advanced race from another planet. The Aschiens tell SG-1 they will gladly share their technology, based on certain conditions. Will this 'to good to be true' ally prove to be just what Earth has been looking for, or do the Aschien have a secret agenda in their offer? The answer they find will shock the SGC to its very core.

A Russian team working for the N.I.D. captures a Jaffa that is being held by the Russians. Another N.I.D. team then captures Carter. The common reason behind these actions revolves around a billionaire named Adrian Conrad. Conrad has a fatal illness, which only the implantation of a symbiote can cure. However, he needs to find out how Carter survived the removal of her former host. O'Neill seeks out the help of the traitor Maybourne to get Sam back before it's too late to save her from Conrad's experiments.

SG-1 find out Martin Lloyd has become the consultant for a television programme similar in plot to what SG-1 do. They also find out a space ship is heading towards the Earth.

After a poor training simulation with new potential recruits for the SGC, O'Neill tries one more exercise, which goes equally bad for the recruits. At the end of the exercise, Jack receives a cryptic call and repeats into the phone the word 'Foothold.' The recruits hearing this know that a potential alien takeover of the SGC has occurred. Jack is then shot, as he shoots andhugs several unknown strangers that arrive in vehicles to talk to Jack. The recruits now appear to be the only people around that can help O'Neill in this situation. They sneak into the SGC through the ventilation system, and try to find Carter, who had warned O'Neill and has the answer to what is happening. However, all is not all what it seems there. And in the end, the recruit team leader, Lt. Elliott, must risk passing to save one of his teammates.

After a near deadly pursuit by gliders and the well aimed destruction of one vessel, the SG-1 team just manage to leap safely through the Stargate. However a glider crashes on the Stargate just as Teal'c is going through, resulting in his energy being trapped in the Stargate. Just how can Stargate Command bring Teal'c through the Stargate?

Daniel Jackson is given a mission by the Tok'ra where he could possibly take out all the Goa'uld leaders.

As Daniel decides to change the original plan tohug the assembled Goa'uld System Lords, Carter must find a way out of the tunnels created by the Tok'ra, which are being destroyed by the attacking Goa'uld fleet. It's up to O'Neill and Teal'c to try to get to save them. In the mean time, back at the Goa'uld conference, Daniel must learn the attending Goa'uld's plans, and escape before he is possible served up as a meal or turned into a Goa'uld at the ending ceremony.

As an asteroid hurtles towards Earth, SG-1 repairs an abandoned Goa'uld ship to use as a launching pad for a naquadah bomb, which should explode the rock into small pieces before impact. But then Stargate Command lose the ship's signal and fear that SG-1 has crashed, leaving them dead and Earth facing a great peril.

Word has spread around Chulak of a formidable new warrior who was once first prime to the Goa'uld, Imhotep. However both Teal'c and Jack are suspicious and Teal'c is told something shocking by the Goa'uld system lord, Lord Yu.

SG-1 investigates a long dead ancient civilization only to find a perfectly preserved female robot. They bring the robot back to Stargate Command and reactivate it in hopes of finding answers to their many questions. However, the robot turns out to have a childlike personality and no memory of what happened to her planet. It turns out Reece, as the robot is named, has a major connection to the Replicators. Can Stargate Command survive Reece's presence on the base? Will this danger spread to the rest of Earth?

Stargate Command learns that a planet with a protective shield against the Goa'uld, and once visited by the rouge off world NID team, is now defenseless against an ongoing Goa'uld attack. SG-1 must utilize the service of two of the NID team who visited the planet, who are also currently condemned to a passing sentence on Earth, to help save the planet. However, can SG-1 really trust the rouge NID team members to do the right thing and help them?

After returning from an off world mission, Daniel Jackson is stricken with radiation poisoning. Attempting to find out what happened, General Hammond hears two different stories, the SG-1 team say Daniel is a hero who saved the people of that planet, but the officials of that planet accuse Daniel of sabotaging a government experiment. Dr. Frasier tells everyone that Daniel is dying and it can only survive if he is put in a Goa'uld sarcophagus.

After the passing of their comrade, Daniel Jackson, SG-1 decide to go on a mission to rescue a stranded Asgard scientist while having to deal with their feelings about what happened to Daniel and the approaching Goa'uld ships.