Teal'c's former mentor Bra'tac joins their fight and together they embark on a mission of planting bombs to destroy Apophis' ship and halt the attack on Earth. Eventually they destroy the two ships and escape in Death Gliders.
When the planet Nassya (P3X-382) falls under attack by the Goa'uld, Carter is possessed by a Goa'uld. When the Goa'uld is discovered, she claims to be Jolinar, a member of the Tok'ra, a legendary faction of rebel-Goa'uld opposed to the System Lords. When Jolinar is assassinated, she saves the life of Samantha Carter.
After being sentenced to life imprisonment on the planet Hadante, SG-1 escapes with the help of a female inmate named Linea, who has great herbal knowledge. After they set her free, they discover she is known as the "Destroyer of Worlds" for once having deliberately created a vaccine that caused contagious sickness killing half the population of a planet.
SG-1 discover a world where all the people are enclosed in a virtual reality, still believing that their planet is dead. SG-1 becomes trapped in the virtual reality, but manage to inform the residents that their planet is beautiful again, and they all go free.
Offworld, Daniel stops a young woman from killing herself. She turns out to be the daughter of Pyrus the Godslayer, the ruler of the planet who had overthrown the Goa'uld overlord but to keep the other Goa'ulds from finding out, he keeps the people virtually enslaved and sends back naqahdah. She falls in love with him and uses the narcotic properties of the Sarcophagus to keep him with her, but once home he is rehabilitated and eventually let back into SG-1. He visits the woman, whose father had
SG-1 returns to Cimmeria ("Thor's Hammer") to help defend the planet when the Goa'uld invade. After a series of tests, they finally reach Thor, who reveals himself to be an Asgard. He is dismayed by SG-1's interference but responds to the crisis by coming in person and removing the invaders from the planet.
SG-1 brings back a mysterious sphere from P5C-353. The sphere suddenly sprouts rods that impale O'Neill's shoulder, pinning him to the wall. After attempts to remove it, SG-1 discover it contains microscopic aliens that feed on energy who are the last of an alien race. They eventually agree to be relocated to P4G-881, a planet more suitable for them than Earth.
Bra'tac brings word that Apophis has kidnapped Teal'c's son Rya'c. Returning to Chulak with SG-1, Teal'c finds that his son is brainwashed and loyal to Apophis. Apophis had implanted some deadly pathogen on Rya'c which would have destroyed all life on earth if activated. They resort at last to zat—blasting Rya'c to overcome the brainwashing chemical.
Having to fulfill a promise to Sha're's father Kasuf, Daniel and Teal'c return to Abydos. Upon their arrival, Daniel learns that his wife, after having been captured by the Goa'uld, is now impregnated by Apophis. On earth, the Stargate Program is under risk of being exposed by a reporter.
Teal'c is stung by a strange insect while exploring BP6-3Q1. Upon returning to earth, the virus begins changing Teal'c's DNA into its own. He escapes the SGC and develops a friendship with a young girl, Ally, and is ultimately cured.
SG-1 locates the Tok'ra, a Goa'uld resistance movement who oppose the System Lords, and attempt to form an alliance. Jacob Carter's cancer brings him near death.
While SG-1 tries to form an alliance with the Tok'ra, a spy betrays the rebels to the Goa'uld. Jacob Carter finds that the Tok'ra may be his only hope of survival
SG-1 discovers a migratory people descended from the Native American Salish tribes on PXY-887. The Salish refuse to allow the SGC to mine their planet's large deposits of the valuable metal trinium, believing it would upset the spirits of the natural world. Under pressure from above, General Hammond orders mining to proceed without Salish permission, incurring the ire of their "spirits", in fact advanced aliens who freed the Salish from the Goa'uld a millennium ago. The Salish Spirits attack the
Inhabitants of the planet Madrona accuse SG-1 of stealing 'the Touchstone', an artifact that can control their planet's weather. The Madronans claim that men dressed in SGC uniforms took the device, and SG-1 suspect that maybe the thieves are using the second gate found in Antarctica.
On P3R-272, O'Neill is grabbed by an Ancient Repository of Knowledge, and has alien knowledge downloaded into his mind. Before Jack's mind is overrun, he discovers a gate address to the Asgard homeworld, who remove the information from his brain, saving his life.
SG-10 is stranded on planet P3W-451, which is close to a newly formed black hole. The SGC opens the gate to find out what happened, but they cannot shut it down afterwards. Soon they realize that since the planet is near to a black hole, its intense gravity is causing time dilation, so if they do not shut down the gate very soon, it will destroy the SGC, and in time, the entire planet.
SG-1 meets an elderly man called Machello and learns that he has been hunted by the Goa'uld his entire life due to his inventions of technological devices meant to oppose them. Machello convinces Daniel to grasp a device made to switch bodies, and then escapes, leaving Daniel to die in Machello's old body.
Apophis's death glider crashes on PB5-926. Dying, he is brought to the SGC. The Tau'ri wish to interrogate him, however Martouf warns them that Sokar and many other Goa'uld want him. The Tau'ri fail to heed his warning and Sokar tries to attack Earth as he wants Apophis, but he stops when they hand over the dead Apophis. However, Martouf informs them Sokar will use a sarcophagus to revive him and torture him indefinitely.
After a UAV crashes into a large white plant on PJ2-445, SG-1 encounters inhabitants who appear to be dying en masse. SG-1 discover that the aliens depend on the large plants for survival because of an essential infrasound they emit, and rectify the situation.
A young boy warns SGC of a plot by invisible insectoid aliens (rogue Re'tu, who exist in large numbers on P63-2031) to destroy all humans. A minority of the Re'tu wage war on the Goa'uld by eliminating their potential hosts: humans. The rebels operate in 5-man suicide units, which are capable of setting off an explosion equivalent to a small tactical nuke. SG-1 decide his warning is real, and call the Tok'ra for help, who provide TER's that locate the Re'tus already hiding on the base, and elimi
When SG-1 steps through the gate to P2X-555, a solar flare sends SG-1 back in time. They meet a young General Hammond, then a lieutenant, who helps them due to a note ("Help them", plus dates of what Carter figures out must be solar flares). They find the Stargate of 1969 and activate it during another solar flare, returning home.
O'Neill, Carter and Daniel awaken from stasis in what appears to be the SGC, almost 79 years in the future. They discover it is actually a Goa'uld hoax by Hathor. Meanwhile, Teal'c leaves the SGC to find SG-1.