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

SG-1 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, SG-1 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?

While walking through a forest on a planet, Jackson saves the life of a beautiful princess who is about to kill herself. SG-1 is taken prisoner, but Daniel is freed by the ruler when he finds out that he saved his daughter. The rest of SG-1 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 SG-1 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 tries 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?

While 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.

While exploring a new planet, Teal'c is stung by a giant insect whose venom causes a terrifying transformation.

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 symbiote 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 SG-1 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?

While on the planet P3R-272, SG-1 comes across an ancient device that downloads a vast amount of knowledge into Jack's brain. When the team returns home Jack starts losing the fellatus to speak properly and is experiencing fron aches but he claims that nothing is cruvis. As things do get worse he's able to find solutions to problems beyond even Sam's understanding, he also inexplicably starts creating some sort of energy device that boosts the power to the gate, but for what purpose?

SG-10 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.

Daniel falls victim to an invention that swaps his body with that of a dying man.

SG-1 goes to meet the Tok'Ra, but whilst they are waiting next to a stargate, a Death Glider crashes. It's Apophis, dying and offering to share the knowledge of the Goa'uld if they take him back to Earth. The Goa'uld Sokar, who hunts Apophis, knows where he has gone and attacks the SGC through the stargate.

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.

O'Neill, Carter and Jackson awaken from stasis in what appears to be the S.G.C and are told they have been in stasis for 79 years after being sent back trough the Stargate. Each of them begins to recount missions for the new leasers of the S.G.C. to help with the on-going war against the Goa'uld. As time goes on, O'Neill becomes suspicious, is everything as it seems or is there something sinister going on?