Jack's second attempt to take a fishing holiday is stopped again when the Pentagon sends USAF Major Paul Davis to call for SG-1's expert help after a Soviet submarine was invaded and its whole crew killed by the replicator which survived the crash of Thor's space-ship and multiplied; Washington needs it handled discretely. At the same time Thor, who is healed, arrives by star-gate to ask help in the Asgard war against the Biliskner which looks desperate, as they only learn from superior technology, so Thor asks 'dumber' help as primitive means like firearms do work; ironically Sam is the one sent with Thor, who shows her the most advanced Asgard ship, their first special war design, called the O'Neill. Jack and Teal'c go inside the submarine with regular troops, finding a whole nest with the survivor bug integrated in a queen; recovering Daniel stays above water with control, but proves valuable there, realizing the meaning of rust on the new bugs... Sam is deliberately not told all the Asgard now, but concentrates on out-smarting the replicators in their way of thinking to devise a trap, which comes at a price Thor is reluctant to pay: sacrificing the O'Neill without any guarantees...

After 3 'impact' events against the iris, the SGC is contacted by humans that are at war and under attack. They plead for help and SG1 visits them. They are technically advanced, living underground in bunkers with much of their population in stasis, protected by shields and remotely piloted aircraft, but all is not as it seems and Jackson asks questions that elicit disturbing answers.

The SGC is visited by Tok'Ra called Anise who brings some armbands used by the soldiers of a long extinct race, supposed to increase the abilities of the wearers. O'Neill, Carter and Jackson put the armbands on and it improves their physical strength, but it also causes them to make rash decisions. can they get the armbands off before they cause their deaths?

An old love of Teal'c, Chulak temple priestess Shan'auc, arrives at the SGC saying she can communicate with her symbiont. Teal'c does not believe her, until he tries and sees that it is true. They travel to the Tok'Ra, as Shan'Auc's symbiont needs to blend with a host, but isn't it really still a Goa'uld?

When an SG member tries to assassinate the Tok'Ra leader, it is believed that some of the SGC have been converted into za'tarc - programmed assassins. The Tok'Ra Anise comes to the SGC with Lantash, to try and test the SG members. But the za'tarc detector suggests that O'Neill and Carter are actually za'tarcs. Is this correct and is there another za'tarc at the SGC?

Colonel Jack O'Neill and Teal'c have a recurring case of déja-vu, but it's much worse, they really recall what happened ten hours ago on SG-1's mission to a planet where a device at an altar near its star-gate throws them back in time, yet Daniel nor Sam recollect anything so SGC refuses to believe them, they're tested, found medically OK, the general calls the mission off when Sam feels it might actually be some time-distortion, but that doesn't work. They learn to be more convincing, so they can go to the planet, but there a certain Malikai proves a problem. Their only hope is to help Daniel decipher the inscriptions on pictures of the altar over many, many time-loops, after Sam helps them make sense of what must be happening; meanwhile Daniel gives them the naughty idea they can get away with pretty much any pranking, as everything reverts to normal unharmed anyhow...

When an attempt to dial out a wormhole fails, the SGC discovers that the Russians have a Stargate and it won't shut down. Together with a Russian expert, SG1 parachute onto the Russian base. They discover that the Stargate is the one lost on Thor's ship. Everyone in the base is dead and some mysterious water taken from a water planet is missing. Three of the team travel to the Waterworld by minisub. Then O'Neill discovers a frozen Maybourne in the freezer.

Whilst on an archaeological dig at the original Goa'uld home world, Jackson is captured by a young Unas. He tries to communicate with it and slowly builds a rapport. Meanwhile, SG1 comes to the planet to find Jackson and they soon realise that some of the SG members there may have been taken over by Goa'uld. Will they be able to discover which ones in time to rescue Daniel.

SG1 are celebrating with the Enkarans they settled on P5S-381, but they receive word that a huge spaceship has destroyed the nearby village and is slowly moving towards them burning the ground as it goes. SG1 try to communicate with the ship and find out that it is 'terra-forming' the planet for a long dead race. A biomechanical lifeform in the ship, tells SG1 that the Enkarans must leave. But they cannot, because they would die. Can SG1 solve the problem in time?

The SG1 team awake to find they have lost their memories. They believe they are workers in an underground power station. They are told that they are helping to preserve life during an ice age. In truth they are slave labor to a huge domed city above and when Teal'c starts to recover his memory and is given another amnesia treatment he forgets his Kelnorim and starts to die. Will the others recover their memories in time to save him?

The SGC is contacted by a strange man called Martin, a conspiricist who believes he is an alien. The question is, how does Martin know about the Stargate and how come he has a gate address and is he being drugged by others?

O'Neill and Teal'c test-fly the experimental spaceship X301, created from two captured Death Gliders. While they attempt a test run in the atmosphere, the craft flies into space. A message from Apophis plays to say that the traitors who took his property would die in the cold of space. Can the SGC find a way to bring them back, or will they die drifting ever further from Earth?

When of Daniel's professors dies in a lab explosion which might be related to the Goa'ulds, he comes back to Chicago to investigate what really happened.

Teal'c is on his home planet, Chulak, where there is rebellion among the Jaffa warriors. He is betrayed as a sacrilegious sholva (traitor) by Rak'nor, son of a Jaffa friend of his father, and handed to Terac, the torturer of system lord Heru'ur. Ignorant of his fate, the other SG-1 members join Jacob in a risky attempt to take hold of a space mine using a Tok'ra ship piloted by Jacob. En route to the Apophis' spaceship, the expedition finds out that Teal'c is being offered as a confidence-building present from Heru'ur to cement an alliance against the other system lords, which would make the Goa'uld threat more dangerous then ever. They decide to save Teal'c but their attempt fails. However Teal'c's resistance to torture and clear conviction that Goa'uld are no gods finally convinces Rak'nor, who now bravely acts.

General Hammond mysteriously retires from the SGC and a new general is brought in, who breaks up SG-1: Daniel and Sam are scientists, Teal'c is with SG-3 and O'Neill commands a new SG-1. O'Neill tries to convince Gen. Hammond to return, but he finds out that someone ordered Hammond to leave or they would hurt his grandchildren. While the others are occupying the new general, O'Neill tries to find out who that "someone" is. Thereto he must place his trust in the one person he hates most: Maybourne.

In 2010, Robert Kinsey is president of a brave new world since he concluded the alliance with the Aschen, a race discovered by SG-1 which lets humanity enjoy its far advanced science and technology, including a vaccine against aging. Sam is now a civilian scientist, married to ambassador Joe Faxon, whose only worry is failing to get pregnant. When she double-checks the Ashen doctor Mollem's computer with Dr. Fraser, who felt superfluous given superior medicine, they discover human fertility is down 90% worldwide in three years. Sam, Daniel and Teal'c turn to retired general Jack, who always warned against handing over technological control, for a daring plan to turn the clock back like general Hammond did once, sending a message to their past with the exact time of a solar flare, which Sam can calculate using the Ashen computer. Only one ingredient is out of their reach: the GDO device to control the Stargate's iris, which is in the White House. Sam implores her husband Joe to steal it, but he has a secret as well as sincere objections...

When a "chosen" boy found on planet Abydos is brought to SGC, he sends a telepathic message, causing Daniel Jackson's personality to undergo disturbing changes. Will the rest of SG-1 be able to solve the mystery of the boy's origin before becomes a power-hungry warmonger?

SG-5's Lieutenant Barber commits suicide by jumping into the Stargate shortly after a mission on a planet where a since about 200 years abandoned Goa'uld palace is studied by Daniel, who soon develops violent mood swings and is committed to hospital with a neurotransmitter brain condition, presumed fatal after all other SG-5 members die; alas meanwhile SG-3 has visited the planet, finding only the light installation Daniel reported as particularly fascinating and human teenage boy Loran, who hid for Daniel's expedition but now tells Jack he was left there by his parents, scientific researchers. Back in SGC, Jack also develops symptoms. Sam and Dr. Frasier conclude it must be some addiction linked to the light, so when Daniel is nearly terminal Jack, who might not have been exposed too long himself, must bring him back. Jack insists to try turning off the light, and leans on Loran, who is looking for a father-figure, even gives Teal'c an early 'birthday present', but indeed has a dark secret..

The chief of staff visits SGC and meets Jack, while Daniel is on a mission. Sam is giving a physics lecture at the Airforce Academy, where she meets and is intrigued by the theoretical insight of US Air Force cadet Jennifer Hailey, academically her successor but a pest in terms of conduct and attitude. When Hailey is about to be expelled for violence against another cadet, Sam convinces the Academy and general Hammond to give her a motivating taste of Stargate work. So they join Jack and Teal'c who are on a planet's moon as security escort to three scientists, but soon find a life-form consisting solely of buzzing lights isn't as inoffensive as it sounds. Sam and Haley come up with incompatible theories; time is running out with the fuel for the generator they need for the only known defense, so Jack makes a barely educated gamble...

After a MALP goes out of remote control, even flying wild, an energy burst during an emergency Stargate shutdown causes serious damage in SGC, and wounds operator Sergeant Siler; Dr. Frasier keeps SG-1 down for check-ups. It soon becomes clear a 'computer program' has entered trough the wormhole, and is taking over the SGC computer network; even after Sam shuts it down, it reemerges, constantly requiring more memory. It not only 'nests' in a hardware constellation it creates, but even manages to take over Carter's brain, and communicates. It's a non-corporeal life form, whose entire home was damaged by a virus caused by the MALP radio waves, and believes its best survival chance is inside Sam, as the humans won't sacrifice her; true soldier Jack however decides to play hardball...

On planet Juna, SG-1 minus Daniel gets a hostile welcome from the local warriors leader Darian, who seems incredulous they even dared to return. They loyally deliver Sam and Teal'c, the particularly hated sho'va (Jaffa traitor) to Cronus (who took over as system lord after SG-1 helped chase Heru'ur) and told them to bury the Stargate. Cronus orders Darian to decapitate Daniel by staff weapon- to find his head is robotic. Cronus's obvious astonishment makes Darian doubt his divinity. At SGC, Harlan urge them to go on a mission. The master robot-creator tells them that the robot versions he created need to recharge after 48. In order to prevent the Goa'uld picking their mind copies, they reluctantly go. Darian now joins them, but feels most of his people won't dare challenge Cronus ever. The two Teal'cs concentrate on revenging the original's father by attacking Cronus recklessly, while the Sams and Jacks deal with the military problems and overthrowing the Goa'uld rule.

SG-1 return to the Tok'ra planet to help them move to a safer planet. Tanith hasn't heard the news of moving to a new planet and SG-1 decide it's time to tell him that they've known all along that he was a spy of Apophis. Tanith escapes his prison and leaves the Tok'ra base. He signals Apophis. When the Tok'ra hear word of this, SG-1 plans a trap. Move the Stargate to a ship and send it towards the sun which will cause a nova explosion, destroying Apophis and his army. Jacob Carter volunteers to send the Stargate to the sun. SG-1 goes with him. As soon as the Tok'ra have left, SG-1 takes the Stargate onto their ship. Soon after the Stargate has been sent toward the sun, Apophis and his ships show up. Two gliders are sent down to the planet to pick up Tanith. O'Neill and Teal'c head toward the planet in their glider and stop the ships from reaching Tanith, but their glider gets hit as well and they land back on the planet. A Gou'ald ship sees all this and heads down to the planet. The Jaffar soldiers pick up Tanith and kill Teal'c. They bring his body aboard, leaving O'Neill alone on the planet. SG-1 picks him up and Jacob flies the ship into hyper speed just as the Stargate hits the sun and explodes. Apophis's army is destroyed. But the effects of the explosion catch up with SG-1's ship and knocks it off coarse. They end up in another universe. Jacob says it will take them over a hundred years to get home, even with hyper speed. Soon another ship comes out of hyper speed. It's Apophis's mother ship.