A year after the first mission to Abydos, Earth's Stargate activates on its own. An enemy named Apophis and his loyal Jaffa kidnap a member of personnel from Cheyenne Mountain. A team led by ColonelJack O'Neill investigates, they reunite with Dr.Daniel Jackson on Abydos. Where soon Apophis returns and kidnaps Skaara and Sha're (Jackson's wife). The team track Apophis to Chulak to rescue their missing comrades.
A year after the first mission to Abydos, Earth's Stargate activates on its own. An enemy named Apophis and his loyal Jaffa kidnap a member of personnel from Cheyenne Mountain. A team led by ColonelJack O'Neill investigates, they reunite with Dr.Daniel Jackson on Abydos. Where soon Apophis returns and kidnaps Skaara and Sha're (Jackson's wife). The team track Apophis to Chulak to rescue their missing comrades.
While Stargate Command and the military decide Teal'c's fate and unbeknownst to the team, a nearly mature Goa'uld is slowly taking control of MajorCharles Kawalsky. With little time remaining, the only way to save him is by careful and potentially life threatening surgery to remove it.
On the seemingly peaceful planet of Simarka, the team encounter a race of Mongol-like Humans whose women have no rights whatsoever. Things turn bad when the team realizes CaptainSamantha Carter has been kidnapped and sold to an enemy tribe, led by Turghan.
After visiting P3X-797, SG-1 discovers The Touched, a race of Humans infected by a disease that seems to devolve them into animal-like creatures. To make matters worse, SG-1 inadvertently brings the disease back with them, where it rapidly spreads throughout the SGC. The only way to cure them is to get a blood sample from the Untouched, who believe the disease to be a curse.
SG-1 is on a mission to retrieve SG-9, who have been declared MIA on Avnil. The team soon discover that leader of SG-9, CaptainJonas Hanson, is posing as the "god" of the planet's inhabitants, who willingly protect him. They must be stopped.
During a search through a yellow-sanded planet filled with blue crystals, ColonelJack O'Neill inadvertently touches one and is knocked unconscious. A double of himself is created to examine the Tau'ri and returns to Earth, where he is set loose to explore Jack's past and soon becomes an unwitting threat to society.
After increased pressure to acquire advanced technology from their missions, SG-1 travel to the planet Gaia in order to capture a creature apparently capable of rendering itself invisible. When Apophis and his guards find them, they are killed, but then miraculously resurrected by the Nox, a race of beings who will not meddle with any of their immediate affairs, especially capturing Apophis.
On a visit to Argos, SG-1 discover that a Goa'uld, Pelops, engineered the Argosian race to live for only 100 days. ColonelJack O'Neill is inadvertently infected with the nanites that cause their rapid aging and grows older by the day, while the team try to stop the process before it is too late.
Whilst exploring Cimmeria, Teal'c and ColonelJack O'Neill are transported to a labyrinth where any Goa'uld, as well as their host, will die if they try to escape. The two nevertheless attempt to find a way out, but are found by an unwanted visitor. Meanwhile, CaptainSamantha Carter and Dr.Daniel Jackson use Kendra, a former Goa'uld host, to guide them to the labyrinth.
Dr.Daniel Jackson sees a video documenting classified experiments from 1945 in which the Stargate was actually activated and Ernest Littlefield, Catherine Langford's love was stranded alone on a planet for more than 50 years. SG-1, and Langford gate to the planet and are surprised to find Littlefield still alive.
In order to learn more about Goa'uldsymbiotes, SG-1 returns to Chulak to retrieve one. Meanwhile, Teal'c finds his family and tries to keep his son, Rya'c, from being implanted with a symbiote.
SG-1 return to Earth, convinced that Dr.Daniel Jackson is dead. While they mourn their loss, they begin to have the feeling that their memories are faked to make it look like he died, and that he is still alive. Their theories turn out to be correct, when Jackson is actually imprisoned by an Ohne named Nem to extract information regarding the whereabouts of his mate, Omoroca.
The Goa'uld queen, Hathor, named for the Egyptian sex goddess, awakens after being discovered in her Sarcophagus in Mexico and makes her way to Stargate Command. She begins to exert her influence on the men of the base in order to start building her new Jaffa army. Soon, with all the males loyal to her, it is up to the females of the base to stop her.
SG-1 arrives on the planet Hanka and learns that everyone, natives and SGC personnel alike, has died from a mysterious disease. They find Cassandra, the lone survivor, and take her back to Earth. They soon discover, though, that she has had a bomb planted inside of her set to blow in a matter of hours - and removing it is impossible.
SG-1 is captured by the inhabitants of Cartago. They particularly want Teal'c, who was responsible for the death of the father of one of the men while he was still First Prime of Apophis. The inhabitants prepare Teal'c for Cor-ai, their version of a trial. Despite being told by Teal'c not to interfere, ColonelJack O'Neill does not want to go along with the process. Soon, Jaffa arrive to take some of the inhabitants as hosts.
SG-1 rescues a group of technologically advanced Humans, the Tollans, whom they find near death on a volcanically unstable planet. The Tollans don't want to share any of their knowledge with the more "primitive" Earth Humans and, because of this, the NID and ColonelHarold Maybourne plan to take them away for study. SG-1 tries to stop the NID by having the reluctant Tollans use their technology to escape.
After fleeing from a planet full of Jaffa, a mysterious power surge from the Stargate separates Dr.Daniel Jackson and Teal'c from CaptainSamantha Carter and ColonelJack O'Neill. Carter and O'Neill discover they've ended up on an ice planet. Little do they know, they are actually closer to home than they think.
SG-1 arrive on the seemingly abandoned planet of Altair and are soon knocked out. When they awaken with seemingly no ill-effects, they hastily return to Earth. There, they discover that they've been turned into androids. To ensure their survival, they are forced to return to Altair to work with the last remaining Altairan, Harlan, who maintains the power systems of the underground city, but soon learn Harlan is hiding something.
The Stargate program is shut down after SenatorRobert Kinsey's visit, but SG-1 still plans to stop the Goa'uld invasion. They gate to what they think is the Goa'uld home world, but soon discover they are on a Ha'tak vessel, lead by Apophis and Skaara, now host to Klorel. The ships are also now heading straight for Earth.
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