The Rakatan ruins were all that remained of an ancient structure built on Dantooine by the Rakata during the height of their Infinite Empire. The temple itself was built as a monument to the power of the Star Forge, a space station in the Lehon system which could be located using the information stored in a Star Map that was housed inside the temple.
After the fall of the Infinite Empire, the building was abandoned and forgotten for thousands of years. Before the outbreak of the Jedi Civil War, Jedi Knights Revan and Malak learned of the existence of the Star Forge after encountering the Sith Emperor in the Unknown Regions on Dromund Kaas and set out to find the Rakatan superweapon on behalf of him and the coming war. They discovered the ruins and accessed the star map located inside. Although the data had been corrupted, the two were able to retrieve the coordinates of other planets that were once ruled by the Rakata. By investigating each world, they hoped to find more relics of the Infinite Empire that would provide clues to the Star Forge's location. Eventually, they succeeded.
Revan and Malak's fall to the dark side of the Force was completed when they became the pawns of the Sith Emperor of the resurgent Sith Empire, who sent the pair on a search for the Star Forge. However, while searching for the Rakatan factory, the two new Dark Lords broke free of the Emperor's mental control, believing his instructions to be their own desires. They would make use of the Star Forge to create fleets of warships with which they would attempt to conquer the Galactic Republic. During the subsequent Jedi Civil War, Darth Revan was captured by a Jedi strike team led by Bastila Shan. His mind was badly damaged during the event and the Jedi Council used the Force to erase all memories of who he was and replaced them with an identity loyal to the Republic.
Following his rescue of Bastila Shan on Taris, Revan was given once again Jedi training, and progressed to the rank of Padawan at the Jedi Enclave on Dantooine. Meanwhile, the Jedi Council had appointed the task of investigating the ruins to Jedi Master Nemo, whose failure was later assessed by Revan and Bastila. Once again inside the ruins, Revan found Nemo's body, and an ancient droid Overseer who guarded the entrance to the Star Map. After cycling through several alien dialects in an attempt to communicate, Revan recognized what seemed to be an archaic dialect of the Selkath spoken on Manaan. The Overseer told Revan that he had to be tested in the proving grounds, in order to prove himself worthy of accessing knowledge of the Star Forge, yet, the Overseer did not provide much information on the topic related to the Builders. It was apparent that the Jedi Nemo had failed the assigned tasks and was killed as a result by the ancient defense system of the temple.
Revan proved himself worthy and activated the Star Map, thus beginning a journey to retrace his own steps towards the Star Forge and there confront his apprentice Darth Malak. An amateur archaeologist by the name of Casus Sandral also made an effort to discover the source of the ancient ruins, and found some correlation between them and something called the "Rak".
Near the close of the Jedi Civil War, a Sith battle group under the command of Malak attacked the nearby Jedi Enclave and destroyed it. During the fighting, the Rakatan Ruins were also bombarded and obliterated, likely in an attempt to prevent others from discovering the Star Forge's location. After the bombardment, a group of mercenaries, led by Azkul, installed a camp near the ruins, though no one possessed knowledge of their significance.