Season three of Stargate SG-1 began airing on June 25, 1999 on Showtime and concluded after 22 episodes. The third season concluded after 22 episodes on March 8, 2000 on British Sky One, which overtook Showtime in mid-season.
Just after Samantha Carter receives a promotion to Major, ColonelJack O'Neill is beamed out of the middle of the ceremony and aboard a ship belonging to Thor of the Asgard. Thor tells him that he will host a negotiation between the Tau'ri and System LordsCronus, Nirrti and Yu. However, one of them does not wish to negotiate.
Dr.Daniel Jackson has hallucinations and is soon diagnosed with schizophrenia, possibly due to excessive Stargate travel. It is not, however, schizophrenia but a Goa'uld killing device belonging to the late Ma'chello. Teal'c then ends up receiving the Goa'uld killing device that Daniel Jackson had.
SG-1 is impressed with the learning power of Orbanian children but soon learns that the children eventually go through a ceremony which removes the nanites from the children in order to take away what they learned. ColonelJack O'Neill decides to take Merrin away from them and teach her how to become a true kid.
SG-1 is captured by Aris Boch, a bounty hunter working for Sokar, and proves to be almost impossible to escape from. He forces them to help him capture a Goa'uld hiding on their planet, but SG-1 soon discovers they are about to capture a Tok'ra.
SG-1's efforts to retrieve SG-11 thought to be MIA gets them stunned and captured. They work out that the "SG team" is actually made of slaves who work for Apophis to invade Earth. SG-1 must convince them that Apophis is dead and to stop them from carrying out their mission.
The Abydonians are kidnapped and sent to P8X-873, which is controlled by Amaunet. As several SG teams rescue the Abydonians, Dr.Daniel Jackson tries to get to Amaunet and save Sha're. However, it does not end the way Jackson wanted.
SG-1 arrive on Vyus and finds the inhabitants have all lost their memories. The team soon discovers that the culprit is someone they had dealings with before.
Martouf tells MajorSamantha Carter that her father is captured by Sokar and sent to "hell", which is actually a prison moon Netu terraformed to make it resemble hell. Carter and the rest of her team plan a rescue but are later captured themselves.
SG-1 discovers that Apophis is a prisoner on Netu and is planning a revolt against Sokar. Meanwhile, Teal'c goes to Vorash to seek assistance from the Tok'ra, but they have plans other than rescuing the teams to stop Apophis.
Little does SG-1 know, mysterious aliens have taken control of Stargate Command and are impersonating the personnel. Teal'c and MajorSamantha Carter notice and escape. While Teal'c tries to stop them, Carter reluctantly seeks the NID to help stop them.
The Tollans ask for SG-1's help when Klorel crashes on their new homeplanet, Tollana. They need SG-1 to help assign Skaara/Klorel's fate. They must perform the triad, where they argue against the Nox and Zipacna of the Goa'uld. Meanwhile, Teal'c and MajorSamantha Carter believe that Zipacna is using the triad to distract them whilst his Jaffa work on crippling the Tollan defenses to enslave Tollana.
SG-1 explore P4X-884 after noticing it to be a paradise world. However after several hours, they return with no memory whatsoever about what has happened. They soon discover a computer simulation named Urgo trying to influence the team. After they find him annoying, they attempt to stop him but find it very difficult to do so with Urgo doing everything he can to distract them.
On Edora, SG-1 convinces the peaceful natives that every hundred years the annual fire rain would have a devastating impact on the planet. However during the evacuation process, an asteroid supposedly destroys the gate leaving ColonelJack O'Neill and a few Edorans stranded. Meanwhile, the rest of the team on Earth spends a hundred days trying to reach them again.
An angered ColonelJack O'Neill steals a piece of technology from the Tollans after they refuse to give some away to the Tau'ri. Major GeneralGeorge S. Hammond later finds out about this and O'Neill soon resigns. During his retirement he is approached by ColonelHarold Maybourne of the NID with the purpose of recruiting him to work for the NID and steal technology from other worlds.
The Bedrosian military are convinced that SG-1 are working for their enemy, the Optricans. While imprisoned, Teal'c evades capture but is blinded. He relies on an archaeologist to help free the rest of his team.
Apophis has taken control of Sokar's forces and is racing the Tau'ri to search for the Harcesis, a child with all the knowledge of the Goa'uld on Kheb. SG-1 gets there first, but it is only a matter of time before the enemy catch up to them.
Dr.Daniel Jackson stares down on a Crystal skull; however, he mysteriously disappears. Jackson tries his best to communicate with them even though he can't be seen. He gets his grandfather, Nicholas Ballard, to help since he claimed to have experienced the same thing.
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