- "Our goal is to take out Anubis' new super weapon. It's what gives him a clear advantage over the rest of the Goa'uld mother ships. Now, we've received word from Teal'c that Yu has pledged to bring the full force of the remaining System Lords' fleet down on Anubis once we've succeeded."
- ―Samantha Carter[src]
The Battle to destroy Anubis' mothership was a series of confrontations with the Tau'ri, Langarans and the System Lords and the forces of Anubis, taking place in 2003, resulting in the destruction of Anubis' mothership.
Earlier in 2003, Anubis attacked Abydos in search of the Eye of Ra to power a new superweapon on his mothership. After a brief battle, Anubis tricked the (then ascended) Dr. Daniel Jackson and SG-1 into handing over the Eye. After they did, Anubis quickly destroyed the planet with his now fully powered superweapon.
Following the successful testing of his new weapon, Anubis quickly decimated the united fleet of the System Lords who had gathered to stop him. After he destroyed the System Lords, the Tau'ri feared he would soon attack Earth, so a plan was devised to disable the superweapon, thus ending his dominance over the rest of the Goa'uld.
Meanwhile in Stargate Command, Jonas Quinn discovered what he thought to be the Lost City of the Ancients in a city called Vis Uban on another planet. Soon after that, SG-1 arrived on that planet and quickly discovered it was not the lost city, but the city of the lost. Upon this discovery, the team found Daniel Jackson on the planet. The SGC then created a fake tablet to lure Anubis to Vis Uban. (SG1: "Full Circle", "Fallen")
Once in orbit around the planet, Anubis deployed his soldiers to find details on the Lost City of the Ancients. While Anubis' Jaffa searched the ruins, Daniel Jackson and Jonas Quinn infiltrated Anubis' mothership and searched the computer for the location of the vent for the superweapon. While Daniel and Jonas searched, Colonel Jack O'Neill and Major Samantha Carter flew an F-302 fighter-interceptor from the surface and engaged several Death Gliders. After the vent is found, O'Neill used the F-302's hyperdrive to bypass the shield and used a missile to destroy the vent and overload the superweapon.
This resulted in the loss of Anubis's chief advantage over the other Goa'uld but he manages to capture Jonas and use the mind probe on him and discover the existence of a powerful variation of Naquadah that was located on his homeworld Langara. To that end, Anubis traveled to the Human world in order to conquer it and use the planet's ore to refuel his mothership's superweapon. He sent down his Jaffa to attack the city and confiscate all the Naquadria.
O'Neill and Carter returned to Stargate Command and informed Major General George S. Hammond that Daniel and Jonas were still on the ship and it entered hyperspace. After contacting the Tok'ra to find the location of the ship, the SGC was contacted by Ambassador Dreylock of Kelowna who informed them that Anubis was attacking Langara. O'Neill and Carter traveled to Langara and used the Short range communicator to contact Daniel on Anubis' ship. O'Neill informed him of the situation and Daniel attempted to free Jonas from his cell.
Meanwhile, Teal'c traveled to convince Yu to help destroy the ship after the superweapon was destroyed. Yu agreed but before the battle ordered Oshu to take his fleet to Chodawwa. Oshu explained that Yu was suffering from old age and Teal'c was able to convince Oshu to contact Ba'al and give command of the System Lord fleet to him. Teal'c then traveled to Langara by Stargate and updated O'Neill and Carter on the situation. O'Neill and the Langarans agreed to the plan and Teal'c sent word to Ba'al.
Anubis assigned a scientist to find a way to control the Naquadria and use it to power his superweapon. After the first test fails and overloads the generator, Anubis orders a search for all data relating to Naquadria. His Jaffa corner SG-1 in a warehouse just after the team found the Data Crystals containing Thanos' research on Naquadria. However, Daniel and Jonas who just escaped from a cell ringed down from the mothership into the building and shot the Jaffa.
SG-1 returned to the Kelownan headquarters but were apprehended by more Jaffa let in by Commander Hale, who had made a deal with Anubis. Just then, a Goa'uld fleet led by Lord Ba'al dropped out of hyperspace over Langara and started to bombard Anubis' mothership, destroying it as it attempted to exit the atmosphere. Anubis himself managed to get away in his personal escape ship. SG-1 managed to use the shake of the weapons fire to get the upper hand and kill the Jaffa holding them but Her'ak escaped through the Stargate. (SG1: "Fallen", "Homecoming")
After the loss of his flagship, Anubis rebuilt his mothership, which led his fleet to attack Earth in order to capture the Lost City of the Ancients. After arriving in the system, he probed the planet's defenses and attempted to capture the Ancient outpost at the planet's Southern Pole. However, his plan was thwarted when Colonel Jack O'Neill activated the Ancient weapon platform in the Antarctic outpost, firing a massive swarm of Ancient Drone weapons that destroyed his fleet. (SG1: "Lost City, Part 2")