The supernova causes SG-1 and Apophis' ships to jump 4 million light years. SG-1 hides from Apophis, but after coming out again, they find Apophis' mothership completely abandoned. It is discovered Apophis and his Jaffa fled the ship after it is taken over by Replicators. They infest the Ha'tak, and furthermore, Apophis has brainwashed Teal'c, and is now working against his team.
Even after Apophis' death, Teal'c is still brainwashed. The only way to break the brainwash is the Rite of M'al Sharran, a ceremony in which the symbiote is removed until the Jaffa makes his or her choice whether they are to die free, or a slave.
SG-1 is forced to abandon ColonelJack O'Neill and the team's fifth member, Lt.Tyler. However, before they can reinforce themselves, they are stopped and pulled off duty, since Stargate Command has no recollection of Tyler. Meanwhile, O'Neill and "Tyler" hide from Jaffa patrols.
A mission to K'tau causes the planet's sun to die out, after the wormhole traveled through it, causing it to be unstable. The Asgard, who protect the planet, aren't allowed to intervene; so the Tau'ri are forced to help them themselves, and some of the natives won't allow it.
After a team from the RussianStargate program goes missing on P2X-338, SG-1 and another Russian team are sent to retrieve them. In their search, they find a mysterious tomb, which housed a deadly enemy, picking off the Russian team members one by one.
The Tollans are somehow willing to give away their Ion cannons to the Tau'ri to protect Earth. Omoc died, and Narim believes he was murdered, which had not happened to the Tollans for several years. SG-1 comes to the conclusion that those two events are connected somehow, and a conspiracy is brewing.
SG-1 makes contact with a technologically advanced race known as the Aschen (a race of people SG-1 from an alternate future tried to warn current SG-1 not to make contact with). While they form an alliance, Dr.Daniel Jackson and Teal'c find clues about the Aschen past.
MajorSamantha Carter is kidnapped by masked assailants, who also took a symbiote from the Russians. The rest of SG-1 do all they can to find her. Meanwhile, she finds out who is responsible for her kidnapping: Adrian Conrad, who is dying and wants to experiment on her, so he can take a symbiote to cure him of all illness, and then remove it safely.
SG-1, especially Teal'c, join a camp full of rebel Jaffa, led by K'tano, who wish to stop the Goa'uld, and have more Jaffa join their rebellion. Teal'c decides to change his allegiance to his people, and the rest of the team suspect that K'tano, the former First Prime of Imhotep, is hiding something from them.
SG-1 finds Reese the last of her people on her home planet. They take her back and soon learn that she is an android. Furthermore, she can create Replicators, and they soon become a serious threat to Stargate Command.
The Goa'uldSystem Lord, Svarog, is planning on taking back Latona to his control. The only way to stop him is the Sentinel, a piece of technology capable of defeating him. Unfortunately, rogue NID agents once tampered with the device, and SG-1 gets the ones responsible to make it operational again.