In 1997, SG-1 visited the planet Altair where Harlan created android duplicates of them. Eventually, Harlan let SG-1 go and the android version of the team agreed to bury their Stargate. Despite this, they eventually began going out on missions of their own and fighting the Goa'uld as the human version of the team does. (SG1: "Tin Man", "Double Jeopardy")
Some time in the past, SG-1 visited the planet Juna and encouraged people to rebel against the forces of the System Lord Heru'ur. Not having seen Heru'ur in person for generations, the people agreed and drove Heru'ur's Jaffa from the planet. Following SG-1's instructions, they then buried their Stargate so that Heru'ur could never return. However, after Heru'ur was killed by Apophis, the System Lord Cronus came to the planet in his ship and took control of the planet for himself, harshly punishing the inhabitants for their rebellion and unburying the Stargate. (SG1: "Double Jeopardy")
Some time after Cronus' takeover, the robot Colonel Jack O'Neill, Teal'c, Major Samantha Carter and Dr. Daniel Jackson arrive on an exploratory mission and are captured by the people of Juna and a Jaffa, led by Darian, but the robot O'Neill manages to escape after being hit by a Zat'nik'tel blast and being presumed unconscious. That night he captures Darian and his wife Hira and tries to explain to them the truth about him and his team and after learning how Cronus took control of the planet, tries and fails to convince them of the truth about Cronus and Heru'ur so he leaves. The next day, Cronus returns in his ship and is pleased to learn of the capture of what he believes to be SG-1. Cronus holds a gathering attended by the warriors of Juna and robot O'Neill disguised as a Juna warrior. As a reward for his loyalty, Cronus orders Darian to kill robot Jackson and has his Jaffa hold the people hostage to force him to do so. Robot Jackson signals robot O'Neill not to interfere and Darian blasts robot Jackson with a Staff weapon, decapitating and "killing" him, but shocking everyone including Cronus as it reveals his true nature as a robot.
Meanwhile, Harlan comes to Earth worried about the robot team as they are overdue and gives the real team (minus the real Dr. Daniel Jackson who is on a mission) the location of the planet they went to. As Stargate Command dials the gate and sends a MALP, robot O'Neill takes out the Jaffa guarding the gate and uses the MALP to communicate with Earth. He is joined by Darian who, after seeing Cronus' reaction, came to realize that he is not a god after all and wants to help. After learning of the situation, SG-1, minus Jackson travel to the planet. On his ship, Cronus orders his Goa'uld scientist Ja'din to find out how the robots work and she "tortures" robot Carter and Teal'c for information on how the deactivated power pack on robot Jackson works.
At the same time the real team comes up with a plan: use the Transportation rings in the Pyramid to reach the ship with the plan to travel to the Pel'tak (the bridge) and seal off the other levels to keep the Jaffa out while they kill Cronus and then offer the Jaffa freedom. On the ship, after being contacted by robot O'Neill, robot Teal'c offers a deal in exchange for robot Carter's freedom, but instead uses the opportunity to attack Cronus, overpowering one Jaffa and killing the other with his staff weapon, though that Jaffa gets off a shot that kills the other, before shooting Cronus who uses his Kara kesh's shield to block it, causing robot Teal'c to start strangling him. Robot O'Neill is taken by Darian to see Sindar, pretending to be a prisoner before the two attack, killing Sindar while the rest of the team enters and helps take out the remaining Jaffa, but robot O'Neill is badly damaged by three staff blasts. Robot Carter tells Ja'din how to reactivate the power pack, but in reality tricks her into activating a Self-destruct that kills her and frees robot Carter, who takes out the Jaffa guarding the rings and transports up the team, leaving behind robot O'Neill and Darian.
Teal'c rushes to the Pel'tak where robot Teal'c is shot in the back and mortally damaged by another Jaffa who Teal'c shots with a Zat'nik'tel then uses as a shield to try to no avail to shoot Cronus before Cronus shoots both the Jaffa and Teal'c, killing the Jaffa and wounding Teal'c, allowing Cronus to begin crushing Teal'c's symbiote to painfully kill him. Robot Carter, Major Samantha Carter and Colonel Jack O'Neill travel to a circuit breaker to close the area off and robot Carter pulls the crystals as its protected by a force field, getting electrocuted the whole time while O'Neill and Carter cover her. Robot Carter successfully pulls the crystals and closes off area, but "dies" from the damage she sustained doing it. On the Pel'tak, Cronus continues trying to kill Teal'c, but robot Teal'c manages to grab a staff weapon and shoots Cronus in the back with it three times, killing him and saving the real Teal'c. Robot Teal'c "dies", proclaiming he did it for his and real Teal'c's father Ronac who Cronus had killed in the same way he tried to kill Teal'c. The invasion ends and SG-1 ends up capturing Cronus' ship, but robot O'Neill "dies" of the damage he sustained from the staff blasts and his power running out. With Cronus dead, O'Neill has Darian get any people who believe that still believe Cronus is a god so they can be shown Cronus' body as proof that he's not. (SG1: "Double Jeopardy")
Following Cronus's death, SG-1 and the SGC gain control of his Ha'tak. They later agree to allow the Tok'ra to borrow it to move to a new planet in exchange for being taught how to properly fly the ship. However, Tanith alerts Apophis who attacks. Using the ship they captured from Cronus, SG-1 and Jacob Carter are able to destroy Apophis' fleet with a supernova and eventually kill Apophis at the cost of the ship. (SG1: "Double Jeopardy", "Exodus", "Enemies")
Cronus' death following soon after Heru'ur's and then Apophis' not long later, throws the Goa'uld Empire into chaos with the loss of the three most powerful System Lords. While this paves the way for an assassination attempt on the System Lords at the System Lord Summit, it also opens the way for Anubis to return to power. (SG1: "Summit", "Last Stand")