Anaxes, a terrestrial planet home to important shipyards, had previously been threatened with destruction during the Clone Wars. In 19 BBY, the final year of the conflict between the Galactic Republic and the Confederacy of Independent Systems, the Separatists launched an attack on Anaxes led by Admiral Trench. The Separatist forces initially had the upper hand due to having gained access to a secret, highly-effective Republic strategy algorithm from a captured ARC trooper, Echo.
After Jedi General Anakin Skywalker, Clone Captain Rex and Clone Force 99 rescued Echo, the Republic launched a counterattack against the Separatists. When it became clear the battle droids were being driven back, Trench activated his backup plan: "total annihilation" in the form of a bomb hidden in the assembly complex which was powerful enough to destroy most of the planet. With the help of Skywalker and Echo, Jedi General Mace Windu was able to disarm the bomb, and Skywalker killed Trench and blew up his flagship, Invulnerable, ending the threat the Harch had posed. However, a Separatist stronghold still remained on the planet.
The Clone Wars ended later that year with the reorganization of the Republic into the Galactic Empire and the destruction of the Jedi Order, which was falsely accused of treason by Dark Lord of the Sith Darth Sidious, publicly Supreme Chancellor and Galactic Emperor Palpatine. The new Emperor promised to bring about a new era of "peace" for the galaxy.
After the rise of the Empire, Anaxes was destroyed in a cataclysmic event sometime during or between 19 BBY and 5 BBY. All that remained of the planet was an asteroid belt. Fort Anaxes, a Republic Military base which had been the Republic's headquarters during the Battle of Anaxes, miraculously survived the cataclysm on a new planetoid which was later designated PM-1203. The Separatist stronghold also survived on the planetoid PM-6986. It was theorized that the cataclysm had been caused by a shipyard main reactor failing and igniting a hypermatter stockpile.
The destruction of Anaxes was first mentioned in Fort Anaxes' StarWars.com Databank entry, which went online after the airing of the Star Wars Rebels first season episode "Out of Darkness," the first appearance of the fort itself.