The Ha'tak vessels arrive over Earth, and SG-1 is captured after killing Klorel. Fortunately, a small team of Jaffa led by Bra'tac is secretly stopping Apophis from taking over the Earth and rescues SG-1 for their assistance.
While on an evacuation mission, a symbiote takes CaptainSamantha Carter as its host and makes its way to Earth in order to leave for another planet. However, the rest of the team finds out and arrests her. She tells the team that she is a member of the legendary Tok'ra and that an Ashrak (Goa'uld assassin) is sent to kill her.
By helping a panicked, planet native, SG-1 gets into trouble and are sent to a prison planet with no way of gating out. Their chance of survival lies on an elderly woman, Linea, who has a terrifying past.
SG-1 is caught and sent away as slave labor, except for Dr.Daniel Jackson who is starting to overuse a Sarcophagus and suffers its adverse effects which are similar to that of drug addiction. When SG-1 is finally freed, they take Jackson back to prevent him from using again.
The Goa'uld has discovered that Cimmeria is no longer protected by Thor's Hammer, which SG-1 destroyed to save Teal'c, and is enslaving the natives. Their only hope is to somehow contact the mythical Thor and his people.
SG-1 explores the rather barren and moon-like P5C-353 and brings back a mysterious orb to study. After realizing it is a threat, ColonelJack O'Neill attempts to throw it through the Stargate and return it to P5C-353. However it takes control of him to prevent this, and infects Stargate Command with a virus.
On a mission, Teal'c is bitten by a bug which overwhelmed the planet's previous civilization. He soon falls ill and his symbiote can't heal him. To make matters worse, the NID takes him away to study the affects of the bite. However, he manages to escape and is on the loose. The race is on to find him, not only to find him first but to prevent a worldwide infestation.
Their only hope for Jacob Carter to survive, and to ensure the Tau'ri/Tok'ra alliance a success, is for Jacob to undergo an implantation of the Tok'ra Selmak. Meanwhile their base is exposed to the Goa'uld via an operative on the inside.
The Tau'ri have discovered Trinium, a superlight yet superstrong element, that could prove useful. However, SG-11 is MIA on the planet on which Trinium is found and are captured by the planet's "Spirits".
While attempting to study the Touchstone on Madrona, they discover it is missing. The Madronans blame the Tau'ri since people in SG uniform took it earlier. Soon after noticing strange weather on Earth, SG-1 comes to the conclusion that the NID is launching secret offworld missions by using Earth's second Stargate from Antarctica stored in Area 51.
SG-10 is trapped on a planet that falls victim to a newly formed black hole. While gating to retrieve them, the gate cannot shut down, and the effects of the black hole are being translated into Stargate Command by the Stargate. The distortion could put Earth at jeopardy at being sucked into the black hole through the Stargate.
ColonelJack O'Neill accidentally walks up into a machine which downloads an entire Ancient database into his mind as well as causing his brain activity to increase. He begins to be unable to speak English but only in a completely new language, Ancient. There is nothing the team can do to prevent the transformation, so O'Neill is forced to go his own way to save himself.
While trying to find the Tok'ra, SG-1 witnesses the crash of a Death Glider piloted by Apophis. After demanding sanctuary from the Tau'ri, they take him back to Earth. Due to his injuries as well as the pain and suffering he caused others, the team finds it difficult to save his life. Worse, an enemy named Sokar demands Apophis from them.
SG-1 finds an aged and dying warrior named Ma'chello whose room is filled with technology that can devastate the Goa'uld. Ma'chello's last chance of survival was to switch bodies with Dr.Daniel Jackson. The rest of the team doesn't notice until ColonelJack O'Neill and Teal'c also switch bodies. Now they must capture Ma'chello to switch them all back before Jackson (as Ma'chello) dies.
SG-1's efforts to communicate with some strange inhabitants causes an outbreak of illness. They soon discover an Unmanned Aerial Vehicle crashed into one of the planet's plants, which hurts and upsets it, spreading the illness to the natives.
A genetically engineered young boy is brought to Earth and talks with ColonelJack O'Neill, who warns him that a group of invisible rebels, known as the Reetou, plan to wipe out all humans in order to defeat the Goa'uld. Unknown to Stargate Command there are five Reetou rebels also hiding in the SGC.
A freak accident involving a solar flare and the Stargate causes SG-1 to gate to the Earth in 1969. While trying to figure out a way back, the team is mistaken for Soviet spies and is being transferred to another facility. However, young Lt.George S. Hammond comes to render assistance so that SG-1 can return to their own time.
ColonelJack O'Neill is awakened from stasis in Stargate Command but finds out he is in the year 2077 and that the rest of his team, and everyone he knew, died. However, he has suspicions that the "SGC personnel" is hiding something from him, which he finds later finds out is a planned Goa'uld invasion of the SGC and Earth.