Carter and Teal'c persuade Dr Weir to let them take the hyperdrive, and go to find Thor, on guard at the Replicators' homeworld , to help Colonel O'Neill. They arrive to find that Thor has turned the Replicators' sun into a black hole, and disintegrated the planet. Thor snatches them from their ship just before it is destroyed by the black hole. Some replicators escape, attack Thor's ship, and snatch Carter. Five is on board the replicators' ship, and tortures Carter to punish her for betraying him [ 6.12. Unnatural Selection ] . When she appeals to his humanity, he claims he loves her, and plunges her into an idyllic rural virtual reality, but she refuses to cooperate. Meanwhile, some System Lords request a meeting on Earth to get help against Baal, who has stepped into the power vacuum left by Anubis, and it taking over the galaxy. Dr Weir must negotiate without letting them know that we probably can't fire again the weapon that destroyed Anubis. In bluff and counter bluff, the System Lords threaten to attack instead. Eventually, they all go home except one, who asks for asylum, because his armies have already been defeated. The escaping Replicators have found the Asgard's new home world, and are threatening to overrun it. Thor snatches O'Neill from stasis, and interfaces his Ancient knowledge-filled mind to the computer, where he designs a weapon, and is then cured of the deadly knowledge by Thor. The weapon defeats the Replicators. Five escapes, leaving Carter behind. O'Neill is promoted to Brigadier General, and put in charge of Stargate Command. Carter is promoted to Lieutenant Colonel. But Five has made a replicator Carter...
A Russian Colonel arrives to joint the Stargate programme, but falls sick. As he recovers, Daniel Jackson starts acting strangely, and has to be shot to stop him. As he recovers, he regains faint memories of being under Anubis' control. The disembodied Anubis is taking people over to try to get through the gate. General O'Neill orders a lockdown. They try to force Anubis to use his powers so that the Ancients will stop him. Anubis takes over Carter, giving him access to the computers, then takes over O'Neill, setting off the self-destruct. Anubis, finally in the body of the dying Russian Colonel, gets through the gate -- but Carter changed the destination, to an ice planet.
Five days before a Presidential visit, O'Neill wonders if if is fit to command Startgate. An alien plant runs riot. SG1, on their first mission under Colonel Carter's command, disappears. Baal clams to have captured them, and demands the System Lord who requested asylum in return. That System Lord gives O'Neill a gate address where there is an Ancient artefact. SG-3 brings back a half-charged power device, that could maybe be used to power the Antarctic Base. However, by killing the rampaging plant, they discover the device has been tampered with. O'Neill sends the System Lord with the device to Baal, saying he can use it to kill Baal. Baal does not return SG-1. However, SG-1 dial in, under attack. They had actually been trapped in a secret cavern of Anubis, and only just managed to get free. Back safe, Carter says the faulty power source is powerful enough to destroy the solar system. O'Neill says that's why he gave the dud one to Baal. O'Neill is now more confident of his command.
SG-1's arrival at a new world precipitates its government in an all-out civil war with religious fanatics who worship the old gods. Daniel is injured and trapped on the planet. He has to coordinate a rescue, and a reoccupation of the military bunker where the Stargate is located.
The scientists have redesigned the alien virtual reality chair [ 2.04. The Gamekeeper ] as a training device. Teal'c tries it, and says it is too easy. It gets its training from the players, and the scientists have been using it. He volunteers to train it to be more difficult. But once inside, the chair picks up Teal'c's refusal to quit and belief that they can never really win, and so won't let him out of the game. The strain is slowly killing him. Daniel joins the game to help Teal'c win.
Teal'c tries living off-base, but keeps getting involved, helping people in trouble. When he intervenes with his next door neighbour's abusive boyfriend, he suddenly finds himself in deep trouble. An ex-NID team who were surveilling Teal'c blackmail Daniel into translating some old Goa'uld in return for providing evidence that will clear Teal'c. Pete [ 7.15. Chimera ] proposes to Sam.
A billionaire business tycoon has evidence about the alien attack on Antarctica [ 7.22. The Lost City ] and threatens to go public. He presents an Asgard on TV -- it's a just a clone body grown from Asgard DNA. Sam, with Thor's help, explains this away as just a special effect. However, he says he has more to show. Sam tries to convince him not to say more, by taking him through the Stargate and showing him another world, and explaining that revelation runs the real risk of provoking civil war [ 8.05. Icon ] . But he's still adamant. However, the executives funded by the rogue NID element discredit him with a financial scandal -- they too want the Stargate kept secret, so that they can exploit it. It looks like jail or suicide are his only options, until Sam offers him a new life on another world.
Teal'c's son has become bethrothed to one of the the Jaffa women warriors [ 7.10. Birthright ] , much to Teal'c's dismay: he doesn't want his son to have to make the same sacrifices that he did. The Jaffa group is now strong, and wants to rise up against their Goa'uld. Teal'c tries to convince them that they should wait until they can rise up against all the Goa'uld, but they are impatient. Their camp is attacked, and their Goa'uld overlord killed in the counter attack. But as Teal's feared, all that happened was Baal moved into the power vacuum. The Jaffa including Teal'c's sone are relocated to another safe planet.
The Stargate is "beamed up" from SGC, using Asgard-like technology. Daniel and Sam investigate Area 51. Teal'c is left stranded, and learns that Jaffa are dying in their thousands. The rogue NID group have got access to Osiris' ship, and are using the Stargate to poison Goa'uld with nerve gas, killing Jaffa in the process. Sam and Daniel manage to track them down and get the gate back -- but the rogue group still have the ship, and the nerve gas.
The Replicator Carter made by Fifth [ 8.02. New Order ] contacts SGC and asks to be destroyed. Sam persuades O'Neill to let her interrogate it. The replicator says she was made by Fifth, but enough like Sam that she has deserted him, and he and the replicators, now immune to the Asgard weapon, are hunting her down. Sam persuades her to find the immunity code, so they can retool the weapon. She agrees, but it appears she is actually secretly in league with Fifth, leading him to the Alpha site. However, when he arrives, she destroys him with the Asgard weapon. There was no immunity -- but now there is, since Replicator Carter has had time to study the weapon. She is now immune, and goes off to lead her replicator brethren in a conquest of the galaxy. Real Carter is devastated that she allowed this to happen.
General Hammond commands Prometheus on a rescue mission to Pegasus, to look for the Atlantis team. On the way they are hijacked. All the crew except Daniel are thrown off the ship. He discovers the hijacker is the criminal Vala [Claudia Black]. Eventually the humans regain control of the ship, but Vala escapes.
The Goa'uld System Lords are looking for new bases in their war with Baal, and one has decided to go to the planet where the Tok'ra dumped Colonel Maybourne [ 6.15. Paradise Lost ] . SG-1 go to warn him, and discover he is the king of the local population based on his ability to predict the future -- but he has been reading the prophecies off an Ancient carving. These say that a group from through the gate will save them from the Goa'uld. The team discover a time-travelling Ancient ship, which, no surprise, they use to destroy the Goa'uld mother ship.
Ex Vice-President Kinsey contacts O'Neill, and says that he has been approached by the rogue NID agents, who want to make contact with the top Russian General. Later, he is taken by the group, and turns up in Russia as a Goa'uld, arrested for trying to assassinate the general. It's all a ploy to convince the Russians that the US administration has been compromised, in order to provoke a nuclear war. The NID team themselves have been captured and taken over by the Goa'uld, who are after the Ancient weapon in Antarctica. However, Carter spots the Russian general is no longer wearing glasses -- he must have been compromised, and his symbiont curing his vision.
A barber picks up a strange blue stone at a garage sale, which gives him visions of SG-1 missions. He starts off telling these as stories to his friends, then writes them up for magazines, but they all get rejected. Over the years, as he becomes convinced it is real, it nearly destroys his marriage, until he gets proof that it is real. [A clever "clips" episode that pokes a little fun as his friends critique some of the plot points in his stories.]
The rebel Jaffa start a coordinated uprising against the goa'uld, but their plans are thrown into disarray as the Replicators also start to attack. Replicator Carter [ 8.11. Gemini ] captures Daniel, to discover his Ancient knowledge, gained while he was Ascendend. Sam and Thor try to modify the replicator gun, and destroy one ship -- but the others adapt immediately, and it is useless again. Ball asks O'Neill for help against the Replicators, and tells him that he is working for Anubis, who knows of a weapon that will destroy the replicators, along with all life in the galaxy.
The rebel Jaffa capture the sacred palace of the Goa'uld, where the Ancient weapon also resides. Sam and Jacob go to destroy it, but then realise it can be modified to kill only Replicators. But they must destroy them all at the same time, so that they cannot adapt. They seek the help of Baal's gate programming skills [ 7.09. Avenger 2.0 ] , to program all the Stargates in the galaxy to open at once. The weapon discharge then propagates through the entire galaxy, destroying all the Replicators, including Replicator Carter and her ship, on which Daniel is a captive.... Baal escapes. All the Jaffa flock to the rebels when they see their false gods overthrown.
The newly reunited Jaffa decide not to destroy the super-weapon until Anubis is defeated. Sam takes her fiancee to see her father. Daniel is in a Limbo diner, trying to decide whether to ascend again. Sam starts to have second thoughts, and goes to talk to O'Neill, but discovers that he is having a relationship with a CIA agent. Daniel discovers that the being offering to ascend him was the one who mistakenly ascended Anubis. The agent breaks up with Jack. Jacob tells Sam that Selmek is dying, and he will die too. Sam breaks off her engagement. Anubis tricks half the Jaffa away from the weapon, and launches a bid to capture it. However, the ascending being tackles him just before he can destroy all life in the galaxy. Daniel returns.
Daniel finds some old writings that indicate Ra had a ZPM in 3000 BC. It isn't there now, so SG-1 go back in time using the Ancient ship [ 8.13. It's Good to Be King ] . But they change the timeline -- Ra takes the Stargate with him so that it can't be discovered, and there is no Stargate command. The team leave a video tape sealed in a stasis jar, and the new timeline find it. Alternate geeky Daniel and Sam are called in to help decipher the artefacts. Sam deduces the location of the Antarctic gate.
The alternate team go through the Stargate only to be captured and to find that Teal'c is still First Prime of Apophis. When they show him the tape, he helps them escape, but kills alternate Daniel, who has been made into a Goa'uld. They go back to 2995 BC, to the time of the uprising against Ra, and stop him taking the Stargate. They also hide the ZPM. The timeline is restored -- but now the ZPM is also there in the present.