The SGC get informed by the Tok'ra that SG-1 are captives, and General Hammond send Colonel Makepeace on a rescue mission. Meanwhile O'Neill gets selected by Hathor as the host for a Goa'uld and Teal'c goes back to Chulak to try to recruit some Jaffa to help save the Jack from Hathor.

With a bit of help from the Tok'ra Selmak, SG-1 discover that the Goa'uld Seth is still on earth, hiding from the System Lords. He's been the leader of various cults throughout the ages, where all the followers get killed. SG-1 find him, true to form, as the leader of a cult in the US. The find out that he uses a substance called "Nishta" which is similar to what Apophis used to brainwash Rya'c and the only way to come out of it is to be given a shock, one which would do no harm to the body but it would destroy the virus, and once its gone, it can't reinfect the same person.

They decide to send Daniel, Jack and Samantha undercover, however, Seth is able to sense the remains of the Sams previous Symbiote Jolinar, and sends them to be executed. However, whilst they are beign taken away, Jack over powers the person that is taking him, and is able to shock him with a Zat freeing him from the control of the Nishta. He supplies them with more Zats which they use to free the others of the Goa'uld control and allows them to escape via an underground passage, however when they try to stop Seth he activates his personal shield and uses a Goa'uld Shock Grenade to knock them out cold.

When they awake they see that the place is about to blow and that Seth has gone, they beam down to the underground passage and try to find him before he leaves. Sam finds him and however he has the Hand device which he uses, however Sam is also able to get one and uses the Naquadah in her blood to kill Seth.

Sam gets a well deserved promotion to Major, with the Secretary of Defence officiating. At the end of the ceremony Jack gets transported to an Asgard ship where Thor tells him that Earth is in danger as the System Lords have decided to come in their ships and wipe them out. Thor tells Jack that the Asgard can't leave a ship there to protect Earth all the time as they have an enemy even worse that the Goa'uld that they are fighting within their own planet's system but they offer to make Earth one of their protected planets within the treaty they have with the System Lords.

The Goa'ulds fear the Asgard but will insist they give up something if the System Lords are to agree, as will Earth. Thor picks Jack to represent Earth and himself to represent the Asgard, and three System Lords will come to Earth to represent the Goa'uld. The Goa'uld that come are Lord Yu, Nirrti & Kronos. They demand that for the treaty to be made, Earth must stop using the stargate and must hand the stargate over to them and not become technologically advanced, to which Jack is angry to hear as is General Hammond.

However things start to go wrong when Teal'c and Cronos are injured by an apparent invisible assailant, and Teal'c is blamed. However the rest of the team figure out what really happened and save both Teal'c and Kronos. Due to this, they decide that they can keep the stargate, however if they go off world, it would be at their own risk.

SG-1 discover 9 Goa'uld all dead for many months. However they were locked from the inside and there was no way the anything got out, and so what killed them was unknown. SG-1 go back to Earth to send a medical team to investigate, taking with them a stone tablet which might have the answers if Daniel can figure out how to work it. When they get back to the SGC Daniel starts hearing voices no one else can and acting very strangely.

Soon after he has to be locked up, and Kinsey blames the Stargate for Daniel going mad and tries to shut it down once more, however, when the SG team visits Daniel he realises whats happening to him when he sees something come out of him go into him. When he tries to tell the others they believe its another delusion. However, after a while Teal'c starts to become sick, his Goa'uld seems to be dieing. With the creature out of his body Daniel starts to become more focused and realises that it was infact not a creature but a machine of a sort created by Michello to defeat the Goa'uld with the side effects of it going into a human being a Schizophrenia. When the doctors come to give him medication, he tries to tell them, and asks them to find out the condition of Teal'c.

With Daniel back, and out of the Mental Asylum, he is able to try and figure out where it came from. When he looks over the catalog of the devices found in Machello's home they find a device similar to one they found locked with the 9 Goa'uld. Upon examination they realise that each device holds 10 of these machines, meaning one remained after killing the Goa'uld which went into Daniel but is now in Teal'c. However before they can do anything else, they go inside Jack, Janet and Sam.

However, Sam seems unaffected by it, and discovers it is because of the unique protein markers left in her body by Jolinar when she died. She gives those protein markers to Jack & Janet who are instantly cured. They then give it to Teal'c and he is saved.

The people of the planet Arbon are happy to trade information and technology with Earth. SG-1 are there studying their culture and one of their children, Marrin is on Earth with a Naquadah reactor explaining to Sam how it works. Daniel and Teal'c also have child companions learning from them but when Teal'c's companion gets replaced Teal'c wants to know why. What he discovers is startling they use Nanites to transfer knowledge to each other, however, once a person shares his knowledge with everyone, they forget everything. Meanwhile Jack gets attached to Marrin and doesn't want her to suffer the same fate.

Using the quantum mirror which Daniel discovered, a Samantha Carter and Kawalski from an alternate reality come to SGC. Their reality wasn't able to destroy Apophis's ships and is under Goa'uld control. They're given permission to stay but Sam starts "quantum fluxing". The only way to save her is by returning her to her reality but to do so is almost certain death but then our Sam comes up with a plan which just might work. They would try to contact the Asgard of their world by using the device which Jack had built, however, they do not know how to use it, but with two Carters, this problem is solved quickly.

Jack also finds out that he and Sam are married in the other reality but was killed by the Teal'c of that reality. When they go to the the alternative reality, they are succesfully able to contact the Asgard who save them from the Goa'uld. The SG team then return back to their own reality and destroy the mirror.

SG-1 get captured by a bounty hunter (Aris Bock) while visiting a new planet. He wasn't looking for them, they were a bonus, he was trying to capture a Goa'uld Kelt'ar for Sok'ar. He offers to set them free if they help him capture Kel'tar - not having a lot of choice they agree. Things get complicated when they discover that Kelt'ar is a Tok'ra not a Goa'uld, a distinction Aris seems unable or unwilling to accept. Can they get Aris to see the error of his ways?

SG-1 find a planet whose civilisation is medieval. SG-1 are taken for demons - Teal'c is tested to prove their innocence - if he dies they're innocent if he lives they're guilty and they'll have to kill them! The people also make regular sacrifices to a demon and SG-1 get chosen as a sacrifice. The demon who comes for the sacrifices is an Unas - one of the Goa'uld's original hosts. He takes the SG1 as hosts along with another women, however Jack other plans for the Unas.

On a routine mission SG-1 discover what appears to be a young, unknown SG team fighting some Jaffa. While trying to help they discover that it is a Goa'uld training ground and the 2 young teams were being trained by Apophis to fight earth. However, they try to convince them that Apophis is dead without causing suspicions however they find that it is much harder to do.

SGC get called to P8X373 by Sha're's father (Kasuf) to free some Abydonians who have been taken their as slaves. Once there Daniel finds Amaunet (the Goa'uld who possesses Sha're) who tries to kill him with her ribbon device. To save Daniel's life Teal'c has to kill her. Back at SGC Daniel keeps dreaming of Sha're.

Through the dreams he realises that Sha're is communicating with her, and telling him not to worry and to look for her son who will be the one that has the genetic knowledge of Apophis.

Exiting the stargate on a new planet they discover a world full of young humans with no memory of anything before "the vorlix" which happened a few weeks prior. They have no old people nor children and only the knowledge they can glean from books. SG-1 get taken to see Kira, who is in charge, and it's she who has rediscovered most of the knowledge they currently have. She volunteers to go back to the SGC with some others to see if a cure for "the vorlix" can be found and their memories returned. Once there Daniel falls for her and she for him.

However, as they try and find a cure, they realise that Kira may in reality be Linea the destroyer of worlds which they released from the Prison world.

Sam's dad is captured by Sok'ar - the Goa'uld who has taken the persona of the devil as opposed to God, and imprisoned on his "hell" moon Natou. The Tok'ra believe Sok'ar is about to launch an attack on the other System Lords and Selmak was gathering information on this. If Sok'ar succeeds it'll be really bad, as having 1 System Lord in charge of all the others means the Goa'uld will be more dangerous, working together instead of each working on their own. The Tok'ra need the info Selmak has, and Sam wants to rescue her dad. Martouf has come to Sam as she has Jolinar's memories and she was the only person to escape from Natou. Martouf has a device to help Sam access Jolinar's memories, so SG-1 and Martouf go to rescue Selmak.

They've found Selmak and Sokar does have a huge fleet ready to attack the System Lords. Unfortunately their plan to escape goes amiss because they are discovered by an enemy they thought was dead - Apophis and Sokar brings forward his attack timetable. Sam, Daniel, O'Neill and Martouf are given the blood of Sokar which makes them susceptible to mind control and Apophis tries to use this to find certain secrets. Luckily, just before they were found out they managed to get the information about Sokar's fleet to Teal'c in orbit around Netu. Teal'c takes it to the Tok'ra. They send him back along with one of the Tok'ra who is to blow up Netu while Sokar is in orbit, even if Sam, Daniel, Jack, Martouf and Selmak are still on the moon. Teal'c isn't one to stand idly by and let his friends die though.

The Tollan Narim comes through the gate in search of Jack and Daniel (despite the Iris, as they have the ability to walk through solid matter) as Skaara who is host to the Goa'uld Klorel has crashed on their planet and Skaara has asked for sanctuary. The Tollan have the technology to give either Skaara or Klorel priority over the body, but both want it to be exclusively theirs. Skaara has asked for help from SG-1 to argue his case in the Tollan Triad. With a neutral party, one of the Nox.

As the triad begins Teal'c realises that the Goa'uld are up to no good, and are tampering with the weapons which defend the planet. However, the Tollan are not prepared to hear and they are told not to spy on the Goa'uld again or the triad would favour the Goa'uld. However, Teal'c is not satisfied, and enlists the help of the Nox to hide one of the weapons.

When the Triad comes to a conclusion, it decides that Skaara is to have control, and so he is taken to have the symbiote removed, however, the Goa'uld representing Klorel orders a ship to attack, which it does and destroys all of the weapons in one go, leaving the planet for conquering. However, as Teal'c had hid one of the weapons the weapon is still active and they are able to use it to save the Tollans from the Goa'uld and the Tollan are in their debt, however they do not agree to giving them technology in return.

SG-1 step through the stargate on a mission to a "paradise" world but step out straight back into SGC's gateroom! They've actually been gone 15 hours although they've no memory of it. Dr Fraiser can't find anything obviously wrong with them but then they start hearing voices, normal food tastes out of this world and Teal'c drinks boiling hot coffee straight from the pot. Things get progressively funnier and more strange as they try to figure out what has happened to them. Soon they discover Urgo a machine of a sort implanted in their brains to allow him to explore the world.

However, when he starts to influence them Hammond gets concerned and takes them off duty. The only way for him to be deactivate Sam figures is to go back to the planet and have the creator take it out. Hammond reluctantly agrees. Back on the planet, the creator is very mad at Urgo for appearing to them as he was meant to stay silent. However he removes Urgo and rather than killing him, he puts him in his own head so he has his company instead as he is alone.

When they get back to the SGC, the don't remember a thing that has happened to them since stepping into the wormhole to have Urgo removed.

While making diplomatic ties with Adora, SG-1 discover the planet is under threat from a meteor storm. They attempt to evacuate the planet but Jack ends up getting trapped by the storm on the planet. He shelters in caves with Lara and her family, when he comes out the stargate is gone! Gradually he adjusts to his new life and starts to realise how much Lara has come to mean to him. Meantime the rest of SGC are doing all they can to retrieve him.

The Tollans will not give Earth any of their technology as they do not trust us to use it against the Goa'ulds and not each other, so Jack, Daniel, Sam and Teal'c go as Earth's representatives to give the case that we can be trusted. The Tollan aren't willing to change their minds and Jack, who seems to be getting impatient pinches some technology despite the rest of the team's objections. He feels we should be taking the technology we need to protect ourselves, with or without the permission of the race it belongs to. General Hammond is not amused and Jack takes early retirement to avoid a court marshal.
He soon gets fed up so when Col Maybourne approaches him with the possibility of leading a Stargate team, and taking technology that might help Earth, he's tempted, even though the whole operation is definitely illegal. Meantime, Sam, Daniel and Teal'c are having to get used to a new commander and the idea that they never really knew Jack

SG-1 go through the gate to P2X416. There they find a scientist who has just uncovered the gate. His society (the Bedrosians) believe that they originated on the planet and have been at war with their neighbours (the Opticans) for many years as they believe they originated on another world and were brought to their current planet through a gateway. SG-1's arrival proves the Bedrosians are wrong. The military arrive and capture Sam, Daniel and Jack and refuse to believe the truth, preferring to believe it is an Optican plot to spread doubt and dissent amongst the Bedrosians, and so want to keep them quiet. Teal'c manages to escape with Nian, the scientist, who is open to the fact that his society might have been wrong, but during the escape Teal'c is blinded.

The captured SG1 members are tortured whilst Teal'c's symbiote slowly heals it. However, it is not fast enough so Nian brings back a device which would help him heal much quicker. Once his eye sight gets better the go to rescue the other team members, and are able to quickly dial Earth on the DHD which they just uncovered. Teal'c takes Nian with him as he is no longer welcome on his home planet.

SG-1 and Bra'tac find Keb, the planet where Amaunet hid the Harsis Child - the child of Amaunet and Apophis who has all the memories of the Goa'uld race. Daniel had promised Sha're he would look after the child and so is very keen to locate him. Apophis is also looking for the child and has also located Keb, he sends his troops to get him.

However when he gets to Kheb he realises that the child is guarded by an Ascended being that would take far better care of the child than himself, and so he leaves the child with her, who goes to another planet as Apophis knows the location and would just send army's to get him.

SG-1 visit a planet which has a huge Mayan Temple, in which is a crystal skull. As Daniel looks into the skull a strange field emerges and engulfs him, Teal'c fires on the skull but Daniel has disappeared! As dangerous radiation was also emitted the rest of SG-1 return to base for medical help. Teal'c later returns to take the skull to see if they can figure out what it did to Daniel. As he takes the skull he steps right through Daniel, who has somehow been knocked out of phase. How can Daniel let them know he is there, and what help can his Granddad be?

Daniel is in the infirmary after having his appendix removed so the rest of SG-1 are on leave. Jack decides to go fishing but as he's trying to persuade Carter to go with him he is taken by an Asgard transporter beam. On Thor's ship he finds it overtaken by strange purple, creatures known as replicators, the rest of the crew missing and Thor seriously hurt. The spider creatures are the "enemy worse than the Goa'uld" that Thor had previously told Jack about. They have taken over Thor's ship and discovered the coordinates of Earth and so want to land there and colonise it.
Thor has called Jack up to help him stop this happening, although he can't send him back again, it's a one way trip. Jack agrees and devises a plan to blow up the ship before it lands and to transport the Gate from the SGC onto the Asgard ship and to use it as a way to escape.