When Sam awakens, she is with Pete and it seems that the past few years were a dream. However, she soon realises that the world she is in, has been created by Fifth, the near human replicator who claims to have fallen in love with Sam.

Mean whilst, Thor brings Teal'c back to Earth and beams Jack on-board. He interfaces Jack with his ship's computer, enabling Jack to use the knowledge of the ancients to build a weapon to destroy the Replicators overrunning Asgard colony Orilla. When they get there, the weapon proves to be effective however, Fifth uses Sam as a hostage and manages to escape.

Back at the SGC, Daniel and Dr Weir realise that the Goa'uld system lords have called for fleet to attack Earth and must force the system lords to stop the attack.

Jack is also promoted as the new General in command of the SGC as is Sam who becomes Lt. Colonel.

When a Russian officer arrives at the SGC and falls ill, he appears to have a contagious disease. He infects Daniel, causing him to become violent and tries to go through the gate. However when he recovers he realises that the 'illness' is in fact Anubis, and he is still alive but in as possession by Anubis, who is alive and wants to escape Earth through the Stargate.

However, they are not able to locate him and in spite of the SGC's efforts to try and contain him, his ability to switch bodies allows him to move around without being found. Eventually Anubis is able to take over Jacks body and manages to reach the Stargate where the Russian soldier who is now dyeing, offers Anubis his body to escape in as opposed to that of Jacks. Anubis accepts but instead of reaching the planet of his choice ends up in an Icy planet.

In his difficult early days commanding the SGC, reluctant Jack is faced by every form of catastrophe known to man, from incarcerated aliens to bunting crises, a kidnapped SG-1 team and the predations of opportunistic System Lord Ba'al.

When SG-1 Go missing Ba'al takes the opportunity to claim that it was him that has taken them, and for his return wants the Goa'uld prisoner that the SGC hold.

With a new administrative sidekick causing more trouble than he's worth, Jack also has to deal with a plant problem in the base as well as the discovery of a ZPM thanks to the Goa'uld prisoner.

SG-1's arrival on a planet sparks a religious uprising that becomes a world war. Trapped while trying to stop it, Daniel takes refuge with the Leda however, the Stargate is in the control of the opposing side, and whilst the SGC make negotiations with the opposing forces, Daniel helps Leda and her side to try to overpower the opposition and take control of the Stargate.

The SGC use the Game Keeper's virtual reality technology to send Teal'c into a virtual reality simulation where the SGC is being constantly attacked by Anubis's Kull Warriors.

However, he soon discovers that he cannot leave, and after facing doubts to whether he can win or not, the simulation starts to become a reality and Teal'c life is put in danger. Every time the game is over, Teal'c is given a shock,

With Teal'c's life in danger, Daniel enters the game and uses a precognition cheat to help Teal'c win, freeing them both.

When Teal'c moves into an apartment off base, he attempts to build a life as a "regular" human however his attempts are thwarted when he becomes embroiled in the troubles of his new neighbour, Krista.

Sam wonders about her life and future with Pete and about the risks that she takes in Gate travel and by involving him in that.

Things are further complicated for Teal'c when he is caught up in a murder mystery and the SGC must help clear his name but it seems that the NID are also involved.

When billionaire Alec Colson threatens to expose the existence of alien life to the world, it is left up to Sam to try and make him change his mind. When they continue to decline the existence of aliens, Colson shows the world a real live Asgard, however the SGC is able to make a cover story and convince the general public that what they saw was nothing but advanced holographic technology.

However, with an Asgard in his midst and more incriminating evidence, they show him the stargate and try and convince him that its a worthy secret, however he seems adamant to tell the world which leads to a secretive organisation known as the Trust to intervene and to try and silence Colson forever.

Teal'c is reunited once more with Bra'tac, and his son Rya'c, but is cut short as the warrior leader Ishta is fraught with danger and difficulty. Ishta's determination to overthrow the Goa'uld Moloc before he can murder more of her sisters leads to her capture and torture at his hands.

In the meantime, Teal'c's son Rya'c has chosen to marry without his father's blessing and Teal'c must try and regain his sons confidence and save Ishta.

In "the heist to end all heists," the Stargate is stolen by what seems like Asgard Technology, and SG-1's investigations point to the shadowy Trust organisation, whose only mandate is to obtain technology at any cost.

The SGC must locate the Stargate and bring down the Trust before they are able to use the Goa'uld killing poison to wipe out all the Jaffa and Goa'uld/Tok'ra that they can.

When Sam's Human Form Replicator double contacts the SGC, she asks to be killed as Fifth is torturing her into doing things she'd rather not. Along with that, she tells them that Fifth is on his way to Earth.

Sam arranges to meet with Humanoid Replicator at the Alpha Site along with the weapon that was used to destroy the replicators, hoping that her interrogation will give important clues on how to defeat the Replicators.

However, the Humanoid tells them that Fifth managed to develop an immunity to the disruptor gun which will allow him to take over the Milky Way, however she can help find a way in which they can modify it to defeat him. Is this a trick or is she telling the truth, is she too using his Humanity against him?

When Hammond and the crew of the Prometheus are stranded on a failing Al'kesh, Daniel is left on the Prometheus alone with a mysterious alien rebel named Vala who seems to have much knowledge about the Goa'uld, as well as a Kull Warriors uniform.

Daniel and Vala battle for control of the ship, but will Daniel be swayed by Vala's claims to need Prometheus to help her embattled people who are facing annihilation by Ba'al?

In the meantime, the Hammond and the other personnel on the Al'Kesh must find away to get of the ship or face certain death.

Whilst on a mission to another planet, SG1 meet none other than, Maybourne who has declared himself King of the inhabitants of the planet and appears to have precognitive abilities with which he is able to tell the population of events before they happening, making them believe in him even more.

However, upon searching of the nearby ruins, they discover the source of his precognitive abilities. They find pillars written in the language of the ancient, and on the pillars is the history of the planet, the past, present and the future, and along with the ruins, they find a Puddle Jumper, a ship used by the Ancients, named by the crew of the Atlantis expedition.

Jack who is angry with Maybourne as usual, orders him to return to Earth, however his people do not care if he was reading from the stone, they serve him, as he has brought order to the land. However, Jack is not happy, and his mood worsens as the Goa'uld Ares comes in a ship to claim the planet as his own, and it is up to SG1 to save the people of the planet, whilst fulfilling another prophecy written in stone.

The relations between the U.S. and Russia are strained, as the Russians start believing that the U.S. administration has been compromised when Kinsey who has now been forced to retire, tries to go to the Russia, but is instead found carrying a Symbiote.

Daniel who had travelled to Moscow to meet with the Russians, is instead detained for questioning and is tested to see if he carries a symbiote. Soon things become apparent that it isn't the SGC that has been compromised but the Russian government.

Ever since Joe, a happily married middle-class father, picked up an odd-looking stone marked with strange glyphs at a garage sale seven years ago, he has been seeing visions of a top-secret Air Force unit commanded by Jack O'Neill, who leads a team through an ancient portal called the Stargate.

The visions start to take over his life, and his life is ruined, as his wife and child leave him, and he is left out of business. He takes it upon himself to find the truth and to find SG-1 and Jack O'Neill whom he has seen in his visions.

The Jaffa's battle for freedom comes close to a climax when they join to take the temple of Dakara, the holy city of the Jaffa, currently under the rule of Ba'al, who is now working for Anubis. The seize the chance to take it when they discover that Anubis has begun to battle the Replcators who are proving hard to defeat.

However, Daniel is captured by the Humanoid Replicator version of Sam who wants his knowledge of the Ancients technology buried deep in his subconscious from the time that he had previously ascended. However, whilst Anubis is busy with the Replicators, Ba'al takes the time to contact the SGC and ask for their help to destroy a weapon located on Dakara which Anubis plans to use to destroy all life in the galaxy, and then create life to his likening.

The free Jaffa, Replicators and Anubis's fleet converge on Dakara to get to the weapon, who will be the first to get it.

The Rebel Jaffa, Ba'al, and the Replicators converge in orbit over Dakara as Sam and Jacob try to calibrate the Ancients' weapon to destroy the Replicators, however they discover that this isn't an easy task.

In the meantime, the humanoid replicater of Sam probes Daniels mind, however, whilst in the process, he is able to access the memories of when he was ascended and uses it to get into Replicator Sam and control the Replicators who have reached both Dakara and the SGC.

Back on Dakara, with the help of Ba'al, Jacab is able to calibrate the weapon and use it successfully destroying all the Replicators in the galaxy, however Daniel who has now been hurt by the Replicator, was also on a Replicator ship which is destroyed in the blast. Is this the end for him... again?

With the Replicators destroyed, and the holy city of Dakara now in control of the Rebel Jaffa, the Jaffa must face the hardest part of the mission. They must keep their ground and prevent Anubis from retaking the city.

In the meantime, Daniel must once again choose to ascend or return to Earth and risk death when Oma Desala gives him a second chance.

In the meantime, Sam and Jack must deal with their personal relationships as they endeavour to define themselves after the loss of important people in their lives.

When Catherine Langford, mentor of Daniel and the person whose father first discovered the Stargate in Giza in 1942 dies, she leaves her collection to Daniel. In the collection, he finds a book, which mentions the ZPM (Zero Point Module) was on Earth in 5000 years ago, but discover that Ra must have taken it when the Stargate was buried.

With the hope of powering Earth's defences in the Antarctica outpost, and forming a stable wormhole to the Pegasus Galaxy, Jack and SG-1 use the Puddle Jumper which is fitted with an Ancient time machine to go back in time 5,000 years to retrieve the ZPM, but something goes terribly wrong, and rather than burring the Stargate, Ra takes it with him, creating a different future in which the Stargate was never found and the Stargate Program never existed.

The alternate versions of SG1 must set things straight, but how can they when they reflect nothing on the SG1 team of the original reality.

The alternate SG1 embark on their mission to change the past in order to fix the future. They use the Puddle Jumper (Called Gateship in this Episode) to travel to Chulak to find Teal'c who they hope will help them.

Jack, Sam and Teal'c are successful in escaping Apophis, however Daniel is taken by a Goa'uld and killed. The remaining team, take the Puddle Jumper back 5000 years once again, to right that which was wronged. They find the Original Daniel, who is the only one alive, and must work together to create another uprising, but must make sure that the Stargate Remains on Earth.