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.
After a mission to Velona, where they find a weapon capable of defeating the Goa'uld, MajorSamantha Carter is followed by an ascended being named Orlin, who warns her not to use the weapon.
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.
On her sixteenth birthday, Cassandra Fraiser falls ill. Soon, they learn that when she was younger, Nirrti experimented on her and other children like her. They have to save her before she will die.
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 is training a group of recruits to prove test their limits when joining an SG team. Training doesn't go very well, so ColonelJack O'Neill plans to motivate them.
After escaping the Goa'uld, and killing Tanith, the Stargate shuts down just as Teal'c is still in the wormhole. Their efforts to halt the Stargate program are threatened, when ColonelFrank Simmons of the NID gives them a 48 hour deadline to save him, or the Stargate program will continue, and Teal'c will die.
The Tok'ra ask Dr.Daniel Jackson to covertly spy on a summit between all System Lords, so the Tok'ra can kill them, but learns that a new System Lord is to join them, one long thought to be dead.
An asteroid is on a collision course for Earth. The Asgard can't help, and the Tok'ra are hard to find, so they return to Revanna to repair a Tel'tak, so SG-1 could deliver a Nuclear warhead to destroy it. However, they soon learn that the asteroid may not be natural in origin.
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 his 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.
SG-1 have discovered that the Langarans have Naquadria, a more volatile version of Naquadah, and they plan to use it as a weapon, since the planet's three nations are on the verge of war. Dr.Daniel Jackson prevents an accident, but is stricken with radiation poisoning in the process, and will die if they don't save him in time.
Following the loss of Dr.Daniel Jackson, Anubis has made his fleet immune to Asgard defenses, and he has captured Thor. SG-1 must assist Heimdall to evacuate all Asgard knowledge from Adara II, before Anubis gets his hands on them.
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