When the Tok'ra decided to abandon their base on the planet Vorash in favor to a new world, they contacted their allies, the Tau'ri, to help them relocate the planet's Stargate using their newly acquired Ha'tak. Thus they would be able to have a world outside the known Goa'uld Stargate network. Wanting to keep the new base location secret from the Goa'uld, they decided that Tanith had outlived his usefulness as an unwitting double-agent. They kept him imprisoned as they moved, planning to remove the Goa'uld from his host Hebron. Unfortunately, Tanith escaped and alerted his new Master, System Lord Apophis. (SG1: "Exodus")
Aware of the imminent arrival of Apophis's fleet, Major Samantha Carter and her father, Jacob Carter then came up with a very dangerous plan. After most of the Tok'ra escaped through the Stargate, they placed it into the Ha'tak and dialed it to P3W-451, a planet very close to a Black hole. Sending the Stargate into Vorash's Star, the gravitational pull of the black hole would create a Supernova which would completely annihilate most of Apophis' fleet. The plan worked well, except that Teal'c did not want to allow Tanith to escape, and chased after his Al'kesh in a Death Glider. Teal'c and Colonel Jack O'Neill crashed on Vorash where they ended up battling Jaffa – Teal'c was shot with a Staff weapon, presumably dying with Tanith later capturing him and bringing him to Apophis as a "gift" while Jack, believing that Teal'c was dead was later rescued by SG-1's mothership. The Star went nova as the team tried to open a hyperspace window to escape. The blast wave sent both SG-1's and Apophis's Ha'taks far off course into another galaxy. Vorash itself and the rest of Apophis's fleet were destroyed.
Trapped in an unknown galaxy, SG-1 had no choice but to contact Apophis, but he wasn't interested in what they had to say and threatened to destroy them. However Apophis opened fire, but not on them. Instead, he fired upon another alien ship, which engaged Apophis' mothership. SG-1 took their chance and made a quick retreat. They escape to the corona of a Blue giant, where they can safely repair their ship. On the ship, the Carters completed the repairs and left the corona. They detected Apophis' ship, yet no life signs emanated from it, so they ringed onto it to get new crystals. On the ship, it appeared that the self-destruct had been activated. Jacob went to deactivate it while O'Neill and Carter went to retrieve the crystals. Soon they detected active Replicators on the ship, which attacked the team on their way to the engine room.
The three ringed back to the Ha'tak and escaped in the wake of the explosion of Apophis' mothership. Afterwards, they brought the hyperspace engines back online when they suddenly detected a Tel'tak, piloted by Teal'c with several Jaffa which, according to Teal'c, helped him escape. Teal'c landed his ship unto the Ha’tak, however, when O'Neill went to embrace him, Teal’c took his gun and, with the other Jaffa, held SG-1 at a gunpoint. Apophis entered and declared Teal'c as his First Prime again.
SG-1 was arrested while Teal'c claimed that he was in the service of Apophis all along, calling his time with SG-1 "subterfuge". Unknown to all of them the Jaffa brought the Replicators unto the ship. As SG-1 tried to escape, Jacob freed them, only to be stopped by Teal'c, imprisoning him as well. Suddenly, the ship unexpectedly exitsed hyperspace. The Jaffa found the engine room infested with Replicators and by mere happenstance, the Replicators also allowed SG-1 to escape their cell. Apophis tried to escape from the Replicators as they killed his Jaffa, forcing him to barricade himself in the Pel'tak.
While Jacob and Dr. Daniel Jackson secured the Tel'tak, O'Neill and Carter tried to subdue Teal'c with some help from a shock grenade. They successfully captured him with a precise but not lethal shot and killed the remaining Jaffa. Teal'c was safely brought aboard the Tel'tak but, without any warning, the mothership entered hyperspace, barring any way to get off the Ha'tak.
SG-1 quickly learned that the Replicators had modified the engines so that the ship far exceeded its fastest velocity by combining into a giant bipedal being, using its energy to power the engines. This also allowed SG-1 to quickly travel back to their home galaxy. However, because of the threat which the Replicators posed, they had to prevent the scourge from ever infesting the Milky Way. So, they planned to use the same tactic which they had used on Thor's ship, the Biliskner by destroying the sub-light engines' controls (causing an uncontrolled re-entry of the ship into the atmosphere).
While Jacob returned to the Tel'tak, SG-1 went to the engine room to lay in wait for the right moment to execute their plan. When the ship left hyperspace right in front of Delmak, they destroyed the control crystals and escaped but were chased by the Replicators. Nevertheless, they were able to get into a ring room and Jacob ringed them to the Tel'tak. They left the Ha'tak, which fell into the planet and was destroyed, thus finally eliminating the evil Apophis for good. O'Neill attempted to convince Teal'c of Apophis's death, only to be left completely stunned when Teal'c, still brainwashed stated that his God, Apophis couldn't be killed. (SG1: "Exodus", "Enemies")
With the sudden death of Apophis, the System Lords once again started their internal struggle for power. The Tau'ri also had a problem to bring Teal'c back into his own self as Teal'c was still loyal to Apophis. Even though Apophis was dead, Teal'c still refused to believe the truth. Knowing that they had a problem on their hands, Teal'c's mentor, Bra'tac was summoned to the SGC to help and was later forced to perform the Rite of M'al Sharran on Teal'c which succeeded in eventually breaking the hold Apophis had placed on Teal'c, resulting Teal'c in returning to normal and pledging his loyalty to the Tau'ri and SG-1 once again. (SG1: "Threshold")