Built on a lone bit of solid ground in one of Dromund Kaas's many marshes, the Temple was built long after the downfall of the Sith Empire following the Great Hyperspace War. While its early history has been lost, it was rediscovered by the Sith during the Light and Darkness War when the Sith and the Galactic Republic fought in the marsh surrounding the structure. The Temple was located in a bog that and was guarded with Watcher statuettes; long after the downfall of the original Sith Empire, it served as a battlefield during the Light and Darkness War.
It wasn't until Darth Millennial, an apostate Sith apprentice who rejected Darth Bane's Rule of Two, found the site that the Temple would come to be inhabited again. Founding the Dark Force religion on Dromund Kaas, Millennial and his disciples claimed the Temple as their headquarters, operating out of it for centuries. The clergymen of this Order, known as the Prophets of the Dark Side were approached by Dark Lord of the Sith Darth Sidious sometime after the fall of the Republic and the rise of the Galactic Empire and eventually were integrated into the Empire as the Secret Order of the Empire.
During the reign of the Galactic Empire, Prophets such as Lord Cronal created horrific Sithspawn such as Gorc, Pic, and mutated Noghri. The Temple served as an elementary training ground for many of the Emperor's dark side servants including Grand Admiral Nial Declann, and was the childhood home of Cronal's oft-abused daughter, Sariss. Following the rift between the Supreme Prophet Kadann and Darth Sidious, the Prophets abandoned Dromund Kaas and fled into hiding on Bosthirda. The Temple remained a place of the dark side, however, and it was within its walls that Kyle Katarn fell to the dark side. Mara Jade fought her way past Sithspawned Noghri and Vornskrs to redeem her Master, barely escaping the world alive.
The Temple would once again be visited by Jedi in 44 ABY, this time by Grand Master Luke Skywalker, Jedi Knights Jaina Solo and Ben Skywalker, and Sith apprentice Vestara Khai who were in search of the hiding place of members of the Lost Tribe of Sith and Abeloth.