The surviving members of SG-1 are lost in the unknown darkness of space and are being chased by Apophis. But before Apophis destroys them, an unknown ship attacks and gives SG-1 a chance to escape. Apophis's mother ship finds them again, but they soon find out that there are no lifeforms aboard. Instead they find an army of replicators aboard the ship and the self-destruct system has been activated. They escape the mother ship just as it explodes. Soon after, they receive a message from Teal'c who has been brought back to life and has escaped the attack on the mother ship. But SG-1 soon finds another problem: Teal'c has been brain washed.

To help Teal'c mind clear again, SG-1 asks Bra'tac to help. Bra'tac removes Teal'c's Gou'ald and Teal'c is forced to remember certain memories of his past. The real Teal'c in the end. SG-1 is glad to have him back.

SG-1 finds a weapon on planet 616. As Carter is inspecting it, a spirit alien interacts with her. But Carter passes out. So the alien follows them back through the Stargate. Hammond believes there may be something wrong with Carter and sends her home. The alien takes the form of a man and calls himself Orlin. He lives with Carter for a while and the rest of SG-1 think she's going crazy. In time Orlin and Carter fall in love. But the pentagon finds out about the alien and surround Carter's house.

In escaping a large contingent of Jaffa, SG-1 is forced to leave behind Jack and Lt. Tyler, a new member of the team. Back on Earth no one can recall Lt. Tyler, so Sam, Teal'c, and Daniel must find a way to save Jack while they are quarantined. Meanwhile Jack and Lt. Tyler struggle to escape the enemy Jaffa.

After a rough ride through the stargate to P39-865, the sun of that planet turns red. Carter deduces that an override of stargate protocols allowed them to create a wormhole through the sun, starting a reaction that will cause the sun to die. SG-1 must now make up for their mistake or P39-865 will become incapable of supporting life.

When Cassandra collapses at home, she is taken to the SGC for treatment. A retrovirus is causing her to emit an EM field and she expresses a need to return to her planet for an initiation ritual. SG-1 investigates and finds a Goa'uld laboratory, probably having belonged to Nirrti, meant for experimentation on the planet's population. They find that the ritual is part of the experiment, a time when Nirrti studies her subjects and cures them when she is done. SG-1 has found a way to cure Cassandra, but now all that remains to be found is Nirrti.

When Chaka, the Unas Daniel previously befriended, is captured by humans bearing Goa'uld weapons, SG-1 go to rescue him. There they find a society in which Unas are treated as slave labor and, in an attempt to free Chaka, Jack and Daniel are taken prisoner.

On a rescue mission to recover Russian soldiers believed missing in action on a prevously undisclosed trip, SG-1 gets trapped in a Goa'uld tomb with a number of decomposed bones. . .and a deadly alien monster with an appetite for human flesh!

After the death of Omoc, the Tollan assert that they are now ready to trade technology with the Tau'ri. Negotiations go smoothly, a little too smoothly. SG-1, with the assistance of Narim, investigate the death of Omoc and the Curia's deception of the Tollan people.

SG-1 comes in contact with an alien race called the Volians, a peaceful agricultural race, who introduce them to an advanced race called the Aschen. With the promise of advanced technology from the Aschen, negotiations are opened up and the SGC prepares to go to one of the possible Aschen home world. When it it realized that the home world might be the one mentioned on a note sent trough the stargate a year earlier, the team becomes suspicious, leaving Daniel and Teal'c to explore a buried city on the planet. As the negotiations continue despite the warnings of O'Neill, Daniel discovers a secret about the Volians past with the Aschen that could have deadly consequences for Earth.

Carter gets kidnapped and taken to an abandoned hospital where two doctors work to study the remains of Jolinar. She finds out that they have a Gou-ald, taken from the Russians, and are planning to put it inside a man named Adrian Conrad, to heal his sickness. They need Carter to tell them how to get the Gou-ald out after he's healed. O'Neill believes the government is involved with Carter's disappearance and contacts Maybourne. Together, with Daniel and Teal'c, they find Carter but also find out that the Gou-ald has escaped inside Conrad's body.

A strange ship is headed towards Earth, and the SGC suspects that Martin Lloyd and his companions may have something to do with it. O'Neill is sent to speak to Martin and is assigned as a military consultant on Martin's new show, "Wormhole X-treme!", which uncannily resembles SG-1 despite Martin once again losing his memory. His former shipmates stall Carter and Daniel by throwing them off the trail and into the hands of the NID.

While SG-1 is conducting training exercises for new recruits, Jack gets a call about a "foothold" situation. Wounded by compromised officers, O'Neill must lead the recruits in retaking the SGC.

Teal'c is trapped in the stargate's memory after the the stargate on the other side is destroyed. The Pentagon gives Carter and physicist Dr. Rodney McKay 48 hours to try and find a way to get Teal'c out. Meanwhile, Daniel and Major Davis are sent to Russia to negotiate for use of the D.H.D. and Stargate the Russians have to keep the SGC operational. O'Neill, with the help of rogue NID agent Harry Mayborne, investigates NID boss Colonel Frank Simmons whose captured Goa'uld, using Adrian Conrad as a host, may hold the key to saving Teal'c.

In a Tok'ra plan to wipe out the Goa'uld, Daniel goes undercover as Yu's servant to release a poison at a meeting of the system lords. Meanwhile a Goa'uld attack on the Tok'ra base leaves the rest of SG-1 with their hands full.

As the Goa'uld summit continues, Daniel finds himself face to face with Osiris. He fools him in the same fashion as he did with Yu, but cannot bring himself to cause the death of Sarah, Osiris's host. He remains to uncover information about the unknown master of Osiris. Lantash, having taken Lt. Elliot as a host, guides the rest of SG-1 in escaping the fallen Tok'ra base.

A large asteroid is discovered on a heading straight towards Earth. If it hits, all life on Earth would likely be destroyed. SG-1 initiates a plan to repair a crashed Goa'uld cargo ship and deliver a naqahdah bomb to destroy the asteroid before it hits.

A new leader has risen among the Free Jaffa, K'tano, former First Prime of Imhotep. SG-1, accompanied by Bra'tac, seeks an alliance between the Tau'ri and the large force he has amassed.

On an alien planet SG-1 discovers an inactive android is the only survivor of the destruction of her civilization. They bring her back to the SGC for study and manage to reactivate her. Things take a turn for the worse when she "makes" a replicator bug for Daniel.

To fix a mistake caused by the fake SG team, the real SG-1 must enlist the help of two convicts. The threat of an approaching Goa'uld mothership stresses the repair of the Sentinel.

SG-1 arrives on P9Y-4C3 in the country of Kelowna, one of three countries in an uneasy state of cold war. Sg-1 investigates the country and discovers that Kelowna's technological level is similar to that of the United States in the 1940s, and that several Goa'uld artifacts were found near the planet's stargate. From the artifacts they find a powerful Naquadah variant called Naquadria, which they are turning into a weapon. An accident leads to the Naquadria nearly exploding and Daniel Jackson saving millions from certain death, but he exposes himself to dangerous levels of radiation. Back at the SGC, Daniel lays dying until Oma Desala, an ascended being the team met on the planet Kheb, appears to him and offers him the chance to ascend.

Osiris engages in space combat with Thor over a violation of the protected planets treaty. Freyr arrives at the SCG bringing news of Thor's death and asking SG-1 to mount a rescue mission to retrieve an Asgard scientist from the planet in question. Upon their arrival Heimdall informs them that Thor still lives and has been taken captive by the Goa'uld. O'Neill and Teal'c transport over to the mothership to rescue him from the clutches of Anubis.