As the ship carrying Klorel and SG-1 arrives in Earth orbit, the team is captured and held prisoner. Meanwhile, the SGC has been alerted to the presence of the ship and another carrying the Goa'uld Apophis. As Lt. Colonel Bert Samuels attempts to convince Hammond that his plan of launching nuclear missiles against the ships will work, SG-1 is freed by Jaffa rebel Bra'tac. After Samuels plan fails, SG-1 and Bra'tac race to come up with a plan to destroy both ships and stop the invasion.

Samantha Carter becomes the hostess of a Goa'uld when she was trying to save the life of the previous host.

SG1 inadvertently help a desperate criminal and is charged and sentenced as accessories to his crime. They are banished to a desolate, brutal penal colony and strike a deal with a powerful female prisoner to help them escape. But is this prisoner hiding something from them?

Exploring a strange and beautiful garden, SG1 comes across a dome containing a race that are connected to machines. The team are captured by the machines and rendered unconscious, but awake to find themselves reliving pivotal moments of their lives, over and over again. Then they discover it is virtual reality and a mysterious keeper appears to persuade them to try different outcomes for the moments. But can the team escape his clutches, when they don't know what is real and what is not?

Whilst walking through a forest on a planet, Jackson saves the life of a beautiful princess who is about to kill herself. SG1 is taken prisoner, but Daniel is freed by the ruler when he finds out that he saved his daughter. The rest of SG1 is sent to work in the mines for the rest of their lives. Jackson falls in love with the princess, but also becomes intoxicated by frequent use of a Sarcophagus. Will he come to his senses before the rest of SG1 are worked to death?

O'Neill and the team return to Cimmeria, the planet where they destroyed Thor's Hammer to help Teal'c escape. They find that the Goa'uld have invaded and many of the people are dead. Can they help to find Thor's weapons to fight off the invasion before they are all captured or killed?

SG-1 discovers an ancient artifact and brings it back to the SGC. Ariving at the SGC, it becomes active, pins O'Neill to the gate room wall, and unleashes a virus into him.

Teal'c's son Rya'c is kidnapped by Apophis and SG1 try to rescue him. When Rya'c is recovered he denounces his father and helps to capture the team. They escape, but will they be able to return to Earth and cure Rya'c?

Whilst O'Neill and Carter head to Washington to be decorated by the President and find a security leak, Jackson and Teal'c go to Abydos (after they unbury their stargate) to see Sha're's father. They arrive to tell him that they have been unsuccessful in finding Sha're, only to discover that she is already on Abydos. But they find that she is pregnant by Apophis and the baby holds the secrets of the Goa'uld.

Whilst off-world, the team is attacked by giant insects, one of which stings Teal'c on the back. The bug has actually implanted a virus that converts Teal'c into a living incubator for hundreds of more insects and Teal'c is being eaten alive. The only way to save him is to capture another venomous bug and create an antidote, but time is running out.

Carter dreams about herself as Jolinar, the rebel Goa'uld who briefly inhabited her body. With SG-1, she travels to a world to meet the other Tok'ra and form an alliance against the Goa'uld. Meanwhile on Earth, Carter's father, Jacob, with terminal cancer, calls General Hammond to his bedside.

The Tok'Ra still need a host for one of their dying leaders; when SG-1 refuse, the Tok'Ra refuse an alliance. Sam is told the blending of symbiont and host can cure cancer. So Sam returns to Earth to tell her father about her real job and offer him the cure if he will be host to a Tok'Ra.

SG-11 does not return from a mission to collect trinium ore. When SG-1 travels to the planet, the mystical Indians there say that the Spirits have captured SG-11. After talking to animals said to incarnate the Spirits, SG-11 is released. Soon after SG teams return to Earth with Indian leader Tonané to seek a mining agreement and many people disappear at the SGC.

A climate control device is stolen from a planet and SG1 is accused of the theft. They have to find it and restore it before the planet freezes. Then weather on Earth starts to unexpectedly change and the team believe that the device has been stolen by rogue NID agents. Will they find it in time and how did the NID travel off world?

SG10 are on a planet when one of the binary stars becomes a black hole. They try to escape by dialing Earth, but fail to get back. The SGC sends a probe and sees the black hole, but then they find they cannot disengage the wormhole and the gravitational effects are starting to effect Earth.

SG1 travels to a Stargate where O'Neill looks into a strange device that downloads information into his brain. Back on Earth, he starts to speak using a strange language. Carter and Teal'c try to find a solution and become trapped on a burning hot planet, when the Stargate fails to dial out. O'Neill solves the problem by designing a solution, but then he designs a device. But for what purpose?

Following on a Tok'ra tip, SG- goes to a planet where they find the hated Apophis, nearly dying and under attack by death-gliders. They get back with him, realizing he was tortured by a rival system-lord, with lasting harm. Apophis demands sanctuary, provided Dr. Fraiser can save his life, at least on account of the human host, but without a sarcophagus the prognosis for his symbiont is lousy; he offers all his Goa'uld knowledge in exchange for a new host, i.e. his life, revealing he was defeated by the terrible Sokar, once supreme system lord till an alliance lead by Ra and Apophis unseated him. The confrontation with Daniel, on account on Amaunet/Sha're and their son Klorel, and with former prime Teal'c, is bitter for all three. The Tok'ra send Martouf, to warn the Taurai must hand over Apophis, but their warning is ignored- until Sokar proves he can bombard the iris with accelerated particles and ultimately cut trough it, so the White House orders his extradition, but before they can he dies, unlike his host, an Ancient Egyptian temple scribe of Amun...

The next planet visited by SG-1 holds an unusual surprise: the only person by its star-gate is an old, sick man, known to Teal'c as Machello, since decades a famous adversary of the goa'uld, who even developed his own technology to fight them, was captured and tortured but escaped. He joins them to earth, but Daniel, who touched his recording device, wakes up in the dying body of Machello, which is only discovered after the alien walked of, given a clean bill of health by Dr. Fraiser, in Daniel's body, determined to enjoy life as an earthling, teaming up with homeless Fred, which soon turns bad... While Machello is searched, the others travel back to retrieve the device, but in the process Jack and Teal'c get body-switched too, and Sam fails to figure out on her own how to reverse it...

While testing new technology, a UAV malfunctions and crashes on a planet. SG-1 goes to determine the cause of the malfunction, but discovers that their presence may be causing serious injury to the planet's primitive inhabitants.

When an incoming wormhole is established at the SGC, the iris is over-ridden and opened. A young boy appears and tells the SGC that they are in terrible danger from a group of terrorists. But these terrorists are invisible creatures and they are determined to wipe out all humans to prevent them being used as hosts to the Goa'uld.

A solar flare sends SG-1 back in time thirty years to 1969. Captured by military police at Cheyenne Mountain, they escape with the help of a young Hammond and then must find the Stargate so they can return to the present.

When Colonel O'Neill wakes up, he is told by new staff everything in the star-base is different because he was just revived after 79 years of cryogenic hibernation, as sole survivor of a disastrous SG-1 mission on a goa'uld-ruled planet. He accepts to undergo a 'high tech hypnosis' to retrieve information of use in the present war against them which is going badly, involving earth's ten endangered colonies on other planets. However Major General Trofsky, the new base commander, and his female assistant tell Daniel and Sam, in different sections, that each of them is the sole survivor: it's all make-believe to probe their brains about the weaknesses of earth and the Alliance of the four races. Meanwhile Teal'c awakes on earth, where it took Dr. Frasier months to save him from death, there was no trace of his teammates and he resigns when general Hammond refuses permission to keep searching. O'Neill hears goa'uld language, gets himself free and discovers to be on a fake star-base, frees Sam and Daniel, only to be stopped by the female Goa'uld system-lord Hathor, who employs both Horus and Serpent Jaffa and demands the humans' help against her rival system-lords...