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After continued skirmishes between the Goa'uld and the Tau'ri which had started the year earlier in 1997, Apophis and his son Klorel took two Ha'taks in a campaign to conquer Earth but thanks to the efforts of Stargate Command's flagship team, SG-1, Apophis's attempts at conquering Earth and enslaving the Tau'ri ultimately failed, resulting in the Tau'ri gaining a huge victory over the Goa'uld.
On a mission to P3R-233, Dr. Daniel Jackson discovered the Quantum Mirror and was transported to an alternate reality, where Earth was about to be overrun by a Goa'uld invasion force, led by Apophis. Daniel discovered that his reality faced exactly the same threat - an invasion coming in retaliation for the death of Ra - and persuaded the alternate versions of several of his friends to help him return to save his own world. Just before the alternate Stargate Command was destroyed, Daniel escaped into his reality with the gate address to the planet in question also in Daniel's possession. Afterwards the mirror was transported to Earth and stored in Area 51. (SG1: "There But for the Grace of God", "Point of View")
Shortly afterwards, Senator Robert Kinsey successfully shut down Stargate Command, considering it a "colossal waste of money". Even Jackson's assertion that the Goa'uld were about to attack Earth had no effect on Kinsey who naively and very foolishly insisted that "God" would protect the United States of America and that the Goa'uld would be no match for the US military. (SG1: "Politics")
Knowing that the slaughter that took place in the alternate reality could happen in this reality, Daniel convinced his team members to violate orders. They then armed themselves with various weapons, activated the Stargate, and traveled to the home of the destroyers.
They found themselves in a large room and, at first, didn't know on which planet they were. Exploring the room, they found a then-unknown type of Goa'uld small hand weapon named Zat'nik'tel, which they took with them. Suddenly there was a strong movement and all the members of the team (except Teal'c) were thrown back. Hidden doors opened and SG-1 hid as Jaffa marched in. They bowed before the Stargate as a large ball rose into the center of it and the Jaffa left. Teal'c explained that the ball was a Goa'uld Long range visual communication device. They soon discovered that they had Gated, not to a planet, but to Klorel's Ha'tak which was in orbit of a planet (thus making a dialing possible). It launched into hyperspace towards Earth after their arrival, cutting off their escape.
SG-1 hid in the Death Glider bay and realized the truth - they were on an attack ship heading to Earth. They also noticed that the Jaffa were heading to a gathering. Sneaking back into the cargo room, they watched a large meeting in which they overheard Apophis unveil his son, Klorel (which had taken Skaara as his host), the leader of this ship for the attack. Colonel Jack O'Neill ordered Captain Samantha Carter and Daniel to plant C-4 all over the ship while he and Teal'c were to grab Klorel, in the hope that Skaara can fight the Goa'uld within him.
They captured Klorel, but Skaara was able to assert control only briefly after one painful shot from a Zat. He apologized to O'Neill since he felt responsible for Klorel's doings, but then the Goa'uld took back the control. When guards entered they surrendered rather than to kill Klorel, who then brought the two into the cargo room and contacted his father. Apophis was pleased, and ordered the immediate execution of Teal'c and O'Neill. When asked if there were any other Tau'ri aboard the ship, Klorel made a typical Goa'uld mistake of overconfidence, declaring "I assure you, father. There could be no more."
Skaara seemingly exerted some influence, as Klorel disobeyed his father's orders and delayed their execution, bringing them to the Pel'tak to witness the destruction of Earth. Carter set a timer on the bombs, and she and Daniel tried to free their friends. They successfully took out the guards, but then Klorel grabbed Daniel, knocked the gun out of his hands, and used his Kara kesh to try to kill Daniel. When Klorel didn't stop, O'Neill was forced to kill Klorel/Skaara.
Looking through the window, they saw Earth while the Death Gliders prepared for launch. Carter prepared herself to detonate the C-4 to end the attempted invasion, sacrificing the lives of SG-1 in the process. Just then, another Ha'tak came into view. Teal'c identified it as Apophis' Ha'tak, and notes that it has defense shields that would not be sufficiently damaged by the destruction of Klorel's ship. Destroying the ship they were on would no longer guarantee that the invasion would be stopped. Jaffa broke into the room and threw a Shock grenade, disabling and capturing SG-1.
On Earth, with Major General George Hammond having realized that the extent of the situation and ordered the SGC to be put on full alert, Area 51 had previously created two "Goa'uld-busters", missiles with stealth Mark 12-A warheads enhanced with the Stargate element, Naquadah. Curiously, the Goa'uld ships had delayed entering orbit, giving the United States of America the necessary time to prepare.
Bra'tac, believed to be a part of Klorel's loyal Jaffa was put in command of killing SG-1, but instead informed them that he engineered the Goa'uld's delay by placing Klorel in a Sarcophagus. He knew Apophis would wait until Klorel arose, hopefully giving Earth's warships time to attack, not realizing Earth did not in fact have any. He originally planned to lead his fighter wing against Apophis in Klorel's name, leading father and son to attack each other's ships in the heat of battle. However, being aware of the humans on board, they would now bond against their common enemy, necessitating a new plan.
Meanwhile, two Goa'uld-buster warheads were launched to destroy the two orbiting Ha'tak motherships; however, they failed to penetrate the protective energy shields on the ships with the shields destroying the warheads in the process and also resulting in the plan that Lt. Colonel Bert Samuels had organized failing.
Bra'tac and SG-1 fought their way to Klorel's command center without raising an alarm, Bra'tac quietly dispatched all the Jaffa guards on the way. On the bridge, Klorel was captured and Bra'tac directed the ship closer to Apophis', but one of the guards seriously wounded Daniel in the process. Daniel ordered Jack to leave him with Jack reluctantly did.
The rest ringed themselves over to Apophis' ship. With Klorel as a temporary hostage, Bra'tac destroyed Apophis' steering console. O'Neill then dropped two Fragmentation grenades into the core of the ship, destroying the shield generators so both ships would be destroyed when the C-4 exploded. Bra'tac was impressed and prepared himself to die, but O'Neill overrode that plan, and directed the team to the Glider bays. Overcoming the guards in the Glider bay, two Gliders, with one human and rebel Jaffa each, launched.
Apophis and Klorel, unable to control either ship, escaped through the rings and the Stargate. In the meantime Daniel had survived, using a Sarcophagus to heal his injuries. With seconds before detonation, he dialed the Alpha Site and escaped. Both ships exploded due to the C-4, ending the immediate threat.
The Death Gliders escaped but were heavily damaged from their proximity to the explosion. The team shared a quiet moment, reflecting on the beauty of Earth. The Space shuttle Endeavour, which Major General George S. Hammond had prepped for launch to rescue SG-1 on the very small chance that the flash of light witnessed on one of the Goa'uld ships (from the first shock grenade) was SG-1 sabotaging the ship. When Daniel arrived and confirmed SG-1 was in those ships, Hammond had the shuttle launched. Bra'tac and SG-1 were then shortly returned to Earth as heroes. (SG1: "Within the Serpent's Grasp", "The Serpent's Lair")
After the battle, Stargate Command was restarted, this time on a permanent basis so that the SGC could provide a defense against any further attacks from the Goa'uld as well as any other future threats. Because of the loss of two Ha'taks and most of his Serpent Guards, Apophis's standing among the System Lords was considerably weakened but Apophis's vindictiveness for the Tau'ri had only grown. (SG1: "The Serpent's Lair", "Family")
This eventually led to his defeat by Sokar. After the Tau'ri sent the deceased Apophis through the Stargate to Sokar, he revived him using a sarcophagus and imprisoned him on Netu. Following Sokar's death in 1999, Apophis took control of his forces and became the most powerful System Lord until he was finally killed by SG-1 in 2001. (SG1: "Serpent's Song", "Jolinar's Memories", "The Devil You Know", "Enemies")
According to Garshaw of Belote, there were Tok'ra spies on board the two ships when they were destroyed. As a result, Garshaw was initially contemptuous of SG-1 for their actions but later forgave them. (SG1: "The Tok'ra, Part 1")
The cover story for the destruction of Apophis' fleet was massive solar flare activity. In 2004, Joe Spencer attempted to use these reports to prove to his estranged wife Charlene Spencer that his visions about SG-1 were real. (SG1: "Citizen Joe")