Awakening from cryogenic suspension, O'Neill finds himself in a futuristic version of the SGC. Doctors hook O'Neill to a device which turns his memories into holograms and then question him for information about races able to defeat the Goa'uld.

SG-1 departs on what should be a routine mission and instead end up on Earth in 1969. They must find a way back home before it is too late.

A young boy gains entry to the SGC and tells the SG-1 team he has come with his mother, a member of the invisible Reetou race. The boy announces that the Goa'uld destroyed his planet Reetalia and now Reetou rebels intend to kill all human beings to prevent possible future hosts.

During a routine reconnaissance mission, the UAV plane crashes into a cactus-like plant. Sent to recover the plane, SG-1 discovers that the inhabitants have begun falling ill, and before long a plague of illness sweeps the race.

Pursued by Goa'uld, Apophis throws himself on the mercy of SG-1. Despite his past evil, SG-1 grants him sanctuary. Apophis, who shows signs of having been tortured, is slowly dying and reveals that he is being pursued by an ancient and powerful Goa'uld named Sokar, the original god of death.

When the SG-1 team stumbles upon the chamber of former Goa'uld enemy Ma'chello, they fall victim to his powerful body-swapping invention. Ma'chello takes on Daniel's body and the young archeologist finds himself trapped in the body of an old and dying man.

SG-10 is on a planet when its sun becomes a black hole, and the Stargate link back to Earth threatens to destroy first Stargate Command and then the entire planet.

While on the planet P3R-272, SG-1 comes across an ancient device that downloads a vast amount of knowledge into Jack's brain. Jack has the task of helping Daniel solve ancient mysteries while trying to save himself from braindeath due to the overwhelming stress.

SG-1 discovers a device on a planet, Madrona, called the Touchstone which seems to have the ability to regulate the weather. SG-1 gets permission to stay on the planet to study the device but when they return it has been stolen and the Madronans blame SG-1.

SG-11 has not returned from its mission to PXY-887, where they recently discovered an element, trinium. After O'Neill becomes injured, Carter leads SG-1 through the Stargate to investigate and to negotiate a mining treaty with the inhabitants.

The Tok'ra turns down a request for an alliance against the Goa'uld because Earth doesn't offer enough rewards to justify the security breach. Selmak, a Tok'ra whose host is dying, requests a human host. Carter suggests her father, Jacob Carter, who is dying of cancer.

Through a dream, Captain Carter sees herself as Jolinar of Malkshur, running through a maze of blue walls and brightly coloured people. She stops at a DHD to dial an address. This, so she claims, is the Tok'ra base. So, SG-1 goes off the contact the Tok'ra. Meanwhile, Captain Carter's father, Jacob, has cancer and it is getting worse.

While exploring planet BP6-3Q1, Teal'c is stung by a strange insect which causes him to become ill and almost die.

Jackson and Teal'c travel back to Abydos to fulfill a promise he made to Shau're's father Kasuf. When they arrive, Daniel learns that his wife, whom he hasn't seen since she was taken by the Goa'uld, is nine months pregnant. The father is Apophis, who plans to use the baby as his new host.

Bra'tac arrives with news that Teal'c's son, Rya'c, has been kidnapped by Apophis. SG-1 must accompany Teal'c back to Chulak to rescue Rya'c.

While exploring a new planet, SG-1 find an orb that sends out electromagnetic signals. Thinking it's a time capsule of some sort, they return to Earth to begin their tests; however, the object begins to heat up among other things.

SG-1 must return to Cimmeria in order to help fight off a Goa'uld invasion while searching for a mysterious hall put there by the Asgard Thor.

When Daniel is being manipulated by an alien princess, SG-1 is forced to labor in the mines.

SG-1 travel to P7J-989, where they discover a beautiful garden and a dome full of strange metallic chambers, each containing an unconscious person. As the team inspects the chambers, they are trapped and knocked unconscious.

After assisting a man that is a fleeing murderer, the team is sent through a Stargate to Hadante, a penal world where brute strength and raw power rule.

While on an off-world rescue mission, Sam becomes possessed by a Goa'uld symbiote.

With SG-1 trapped on Klorel's ship, it seems that Earth is doomed as the pyramid ships prepare to destroy Earth.