Jacob and Sam had destroyed most of Anubis's army, however, in doing so they had also become stranded, and with max hyperdrive, it would take them 125 years to return to Earth. Still in their stolen Goa'uld mothership, they see Apophis' mothership arriving, also having escaped the blast from the super nova. The ship SG-1 are on is badly damaged and has no defenses, Apophis is about to attack them when all of a sudden another ship arrives and starts attacking Apophis! SG1 decide to run whilst they still can. However, they retun later to find that Apophis's ship seems to be deserted, and in the attempt to find some salvagable parts, with which they can repair the ship they go on board. However, once on board they discover it's the Replicators who taken over Apophis ship! It's autodestruct is set so SG-1 get what they can and leave, quickly! Then they get a message from a peltak ship and it's Teal'c! who is alive after all. They let him on board only to discover that Aphophis has affected his mind and he believes he's still his First Prime and he had been working undercover for the past four years for Apophis. Things get start to get better when the replicators start to take control of the ship, increasing the maximum hyperdrive speed to a level with which they are able to reach Natu in a matter of minutes. SG1 decide that they will defeat Apophis once and for all, and hopefully the Replicators that are on the ship so that they can't get a foothold in their galaxy.

Bra'tac is brought back to help regain Teal'c mind. He conducts a Jaffa process called "The Rite of Masuraan", which literally means bringing a Jaffa warrior to the Threshold of Death and let him choose the path from there. Teal'c is made to re-live several episodes from his past and we follow his journey to the point where he becomes Apophis's First Prime and re-live the moment where he realises that maybe Apophis isn't a god.

After arriving on an alien planet doing a survey Sam passes out for no apparent reason. Back at base she's told to take it easy and when she gets home she finds she's brought a visitor with her, an alien. To start with no one else can see the alien and they all start to think Sam's gone crazy. However, when after a week of surveylence they didn't see him, they remove the camera's and he appears again. Eventually he takes human form and tells her how he fell in love with her. He tells her about the weapon on the planet and tells them that if they activate it the others will stop them, and even though sam tries hard to stop them, Simmons a man that has been sent by the Pentagon insistst hat they reactivate the weapon. When they decide to finally activate the weapon, Simmons confronts Sam at the SGC about how they know the Alien is in her house, as they seem to have left a few of the camera's behind. When Sam gets home she sees her house is cornered and they want him to come out. Sam goes in telling Simmons that she will get him out, to find that her visiter has built a gate out of various materials, which would work once only. They use the gate to go to the planet where the testing is happening in an attempt to stop it.

Colonel O'Neill and Lieutenant Tyler are ambushed by Goa'uld forces and trapped behind enemy lines, fighting a faction under an unknown System Lord. Meanwhile the rest of SG-1 return through the gate to fetch help. The problem is that when they get back no one else knows who Lieutenant Tyler is! Sam, Teal'c and Daniel are quarantined and General Hammond can't send anyone else back though the gate to rescue Jack in case they get infected. Colonel Simmons uses it as an excuse to question the rest of SG-1 and finds fault with General Hammonds running of the SGC. Meanwhile on the planet Jack is looking after Tyler who was injured and they are bonding while fighting off the Jaffa, turns out Tyler is part of an alien race, that can make others believe they are someone else, and due to this the Jaffa are after them. He tells Jack after seeing him risk his life for him, however he doesn't care if hes an Alien and still wants to help him. Dr Fraiser is able to find out about the chemical which causes the memories of the alien which allows Hammond to send a rescue mission.

SG-1 visit another world, Katal which is an Asgard protected planet. Trouble is to get to the planet they have overridden the safety protocols of the Stargate which means they go right through the world's sun, depositing some heavy elements there which affects the sun's reaction and causes and ecological disaster on the planet, turning the sky red. It was an accident but SG-1 feel responsible. When SG-1 go to ask the Asgard for help, Freyr, the Asgard pretending to be their god allows them to meet with the Asgard High Council. However, they decide that they cannot do anything about it as it would nulify the treaty with the Goa'uld, meaning they would be free to attack all the protected planets. Carter makes a plan to send another more stable element into the sun using a rocket, however things go bad when the local people sabatage the rockets killing two of their men. Even still they decide to help by trying to make the element pass through the sun like they did when they first visited. When it becomes apparant that it didn't work, they start to walk away, however suddenly the sky started turning to the normal colour. It seems the Asgard were able to help after Sam was able to give a viable reason to why the planet was saved.

Cassandra the girl whose village was wiped out by Nirrti is growing up as Dr Fraiser's adopted daughter. However, on her birthday she suddenly starts to develop abilities, however the rate at which shes developing them, she would most likely die. When the team go back to her planet to find a reason to why this is happening they discover that Nirrti was experimenting on the people of that planet to find the perfect host, a "Hok'tar" aka Advanced-Human. Mean while, Cassandra starts to get worse and develops telekenisis with which she can control magnetic fileds and objects. However, when SG1 return back to the SGC after beign unable to find anything in Nirrti's lab, they uknowingly bring an unwelcome guest.

When Chaka, the Unas that Daniel made friends with when he took Daniel prisoner, is captured by people from another world, Daniel wants to go to save him. Luckily General Hammond agrees and SG1 are sent to save Chaka. Once there they discover that the people of the planet use the Unas as slaves as the Unas did once under the control of the Goa'uld. They want Chaka for "fresh blood" as their Unas have inbred so much they are going weaker. They won't let SG-1 take Chaka back and they capture Daniel and O'Neill when they try to break the Unas out of prison, and they imprison them! Carter and Teal'c try to free them and succeed but when they get to the gate Chaka does not want to go with them but stay and free his fellow unas.

SG-1 team up with a Russian unit on a rescue mission to find a Russian Stargate team that went missing off world before they stopped using the gate. They find and investigate a Babylonian crypt, meeting an ancient Babylonian god, Marduk, who turns out to be a particularly nasty Goa'uld. The team they have gone to rescue is dead and the Russians have their own agenda which threatens the lives of both teams.

SG1 go to Tollana for the funeral of Omoc, one of the first Tollans that SG1 met. Narim warns them that Omoc was concerned that Earth was in danger and when the Tollan suddenly seem more than willing to let Earth have access to it's superior technology after the death of Omoc they start wondering why. It turns out that things are not what they seem when they discover with the help of Narim that the Tollans are creating a weapon with the Phase shift ability, allowing them to send the weapons through solid objects, including the Iris protecting Earth. They soon discover that Tanith who is now working for another Goa'uld is behind it, and has ships which portect him from the Tollan weapons.

This is a sequel to 2010. SG-1 encounters a new world and a potential new ally in the war against the Goa'uld. It is a race of people introduced to SG-1 by the people of an agricultural world - the race is the Aschen! SGC discover that their homeworld is most probably the one the future O'Neill told them to lock out of the computer. SG-1 start investigating and Daniel and Teal'c discover an underground city which the people of the world don't know exists and they wonder how, in a couple of hundred the people of the world have gone from millions technologically as advanced as Earth to hundreds on an agricultural world, it can't be coincidence that it only happened AFTER the Aschen came on the scene. They manage to figure it out and save Earth, again, but Kinsey isn't pleased to have to forgo another powerful friend.

When Major Samantha Carter is abducted by mysterious men in black, General Hammond authorizes the rest of SG-1 to go and find her. They need the help of Maybourne the ex-airforce colonel who sold information about the SGC to the Russians. Turns out Maybourne has sold a Goa'uld larva to a rich and powerful private individual. The Russian had captured a Jaffa warrior on their second mission which is where the larva came from, and some renegade Russian soldiers sold it to Maybourne. The man who buys the Gao'uld is dying and wants to use the healing properties of it to save himself which is why they capture Sam so they can see how she survived Jolinar. Maybourne helps them to track Major Carter to a hospital where dangerous experiments are being conducted, but things have moved along and the Goa'uld is implanted in the sick man. With the Goa'uld in charge he escapes, Jack finds him but he escapes again when someone shoots Jack in the back.

SGC find a spaceship heading towards Earth and it's signature is that of the alien spaceship they've encountered before. It belongs to Martin Lloyd who is an alien who ran away from the battle with the Goa'uld with a few other people. They find that he has pitched a script to a television studio, which reads suspiciously like the Stargate scenario. The Airforce let it go so they have "plausible deniability". Jack is sent to confront him to find out why the ship is coming to Earth. When he gets there he finds Marty has lost his memory again, and he and Teal'c must work with Martin on the show. Jack as the Airforce consultant on the show and Teal'c as a caterer, while Sam and Daniel do surveillance. (Note: Stargate SG-1's entire team of writers and producers worked together to pen this special 100th episode.)

The SGC, once a month, has a program to train academy graduates where promising young officers are sent in teams to SGC and a different SG team puts them through their paces, giving them a feel for what they will be faced with when offworld. The idea is that the most promising ones get to join SGC. This time it's SG1's turn. One of the trainees is Cadet Hailey and 3 others. They feel that Col O'Neill is being particularily hard on them and they don't seem to be doing too well. Then disaster strikes, a foothold situation and the trainees are thrown in at the deep end with only Col O'Neill to trust, and possibly Major Carter - Daniel looks like he is the leader of the SGC "turned bad". Col O'Neill is injured and it's totally up to the trainees to try to destroy the device that is influencing SGC and close the gate. Can they do it in time or is it asking too much of them?

Disaster strikes when SG-1 go rushing through the Stargate to escape 100s of Jaffa but Teal'c delays his return to blow up Tanith's ship, which then crashes into the Stargate trapping Teal'c in transit. Sam theorises that Teal'c's "pattern" is trapped in the Stargate and that if they can somehow initialise it they can retrieve him. They can't use the gate to send anyone through or back as that would wipe Teal'cs pattern from the buffer, so they seal the iris inside the gate so no one can dial in. Col Simmons comes and tells them they only have 48hours to get Teal'c out, and brings with him a very annoying scientist who the Pentagon think is the top blocke on Stargate science who says after 48hours Teal'cs pattern will degrade. Daniel and Major Davies go to Russia to see if they can use the Russians gate to bring in the SGC teams that are off-world, and send one to see if they can get help from one of their Allies, and then they ask to use the Russians DHD - but the Russians want alot in return - can they reach an agreement to save Teal'c before the 48 hours are up? Meantime, Jack and Maybourne track down the Goa'uld that had been captured by Col Simmons in Desperate Measuresand try to find out if he knows how to get Teal'c out of the buffer.

SG-1 and the Tok'ra learn that the remaining Goa'uld System Lords are negotiating an alliance, as someone is taking advantage of the places left by the System Lords SG-1 have killed and is attacking all the other System Lords. The Goa'uld taking advantage of the choas is Anubis, but no one knows that yet - just Osiris when Lord Zapacna recruits her to their cause. Zapacna knows where the Tok'ra are and send ships to bomb them. Meantime Dr. Jackson agrees to go in as a Goa'uld's most important human slave so he can use a Tok'ra weapon which kills the symbiot. He achieves this as the Tok'ra also supply him with some mind altering drug which they sythesised from the sample gained from the alien being that they previously encountered, which allows them to influence the mind by making them beleive they are someone else, which makes Yu think that Daniel is his slave. As no other System Lord knows who Daniel is, he would be safe, however, things do not turn out as planned as Osiris in the body of Sarah, an ex-girlfriend.

Daniel injects Osiris with some of the mind altering drug and she thinks he's Yu's servant. Then Daniel talking to Selmak explains he can't use the Tok'ra weapon as he doesn't want to kill Sarah but Selmak convinces him it's the right thing to do. Daniel goes back to the conference but discovers that Osiris is working on behalf of another Goa'uld who is great and powerful - Anubis- he now can't use the weapon as if he kills all the System Lords then Anubis will be the greatest and it's worse having one Goa'uld in control than lots fighting for power. Daniel also finds out that Zapacna knows the location of the Tok'ra base and is going to attack it. Daniel tries to capture Osiris so the Tok'ra can take the Goa'uld out of Sarah but the plan misfires and Osiris ends up knifing Yu, and Daniel escapes and he and Selmak go to see if they can warn the Tok'ra. Meanwhile the Tok'ra base is destroyed along with most of the Tok'ra, the young Lieutenant is badly injured blended with Lantesh who was the symbiot of Martouf, but who is himself not strong. Daniel and Jacob go to rescue them but crash on the planet full of Jaffa.

Earth finds itself threatened by something even larger than the Gou'ald when the team learns that an asteroid is on a collision course with the planet. They decide to blow it up before it reaches earth and so they send SG1 on a Goa'uld Cargo ship with a bomb. However once there they discover the asteroid is not what it seems and that it is infact made from Naquadah and blowing it up would just taking out the solar system. They must now think of a way to get it out of earths path.

A charismatic Jaffa leader Ka'tano, tries to rally his people against the Goa'uld. Brat'ac and Teal'c think an alliance with Earth would benfit both sides. SG-1 go with weapons, medicines and food and offer an alliance but the more Jack sees of Ka'tano the more suspicious he becomes. Ka'tano was the first prime of Imothep and killed him, he seems to know no fear, teaches the Jaffa not to fight to survive but to die, and sends many on suicide missions. Jack thinks he just wants power for himself but Teal'c thinks he's great, they feel it is a cultural thing that Jack doesn't understand. When Ka'tano sends Teal'c on a mission he's unlikely to suceed at Jack says he wants none of it but before they can leave Teal'c returns, with disturbing news for all!