The Crystal Cave was situated at the southeastern edge of the Khoonda plains within the Sandral fields, located on the planet of Dantooine. Around 4016 BBY, the Jedi Order gained exclusive access to the world's abundant supply of valuable crystals, which were crucial for constructing the Order's lightsabers, after Jedi Master Vodo-Siosk Baas established the Jedi Enclave there, marking the discovery of the caves.
On the planet of Dantooine, the Crystal Cave had been excavated by the kinrath, a species of poisonous arachnoids that are non-sentient. The original entrance to the cave was positioned at the eastern end of the Sandral Grounds, named after the Human Sandral family who had built their estate in that region. Sometime after 3956 BBY, the original entrance was blocked off, but the kinrath gradually created a new passage leading to the Khoonda plains, an area that once contained the Matale family's compound. Initially, the Crystal Cave was composed of a single large tunnel terminating in a single chamber. Following the kinrath's creation of a new, larger cave, it came to include two chambers along with a more intricate system of tunnels.
Among the naturally occurring crystal formations were the scarce Adegan crystals, which were previously thought to grow only on Adega, and produced blue, green, and yellow variations. Red crystals sometimes formed inside unhatched kinrath eggs, which was a puzzle for the Jedi; rubat and bondar crystals were also occasionally found within the cave system. In the fourth millennium before the Galactic Civil War, at least one Ultima-Pearl was discovered, even though these gems were typically located on the ocean floor of the planet Dac.
The Jedi Order members who accompanied Jedi Master Vodo-Siosk Baas to Dantooine discovered the caves, and these Jedi established the Jedi Enclave close to the cave entrance to protect its valuable collection of crystals, which were essential for building Jedi lightsaber weapons. As the academy expanded, Jedi pilgrimages became more common, and navigating the caves became a rite of passage, similar to the experience on the Jedi fortress world Ilum. The cave, excavated by the dangerous kinrath native to Dantooine, utilized the tunnel system as a nesting area and would attack anyone they considered a threat to their nests.
During the Jedi Civil War, a conflict between the Republic and the Sith Empire led by Darth Revan and Darth Malak, the Enclave's student population decreased, and the kinrath population in the Caves greatly increased because the Jedi could no longer control their numbers. After Revan was retrained as a Padawan and suffered forced amnesia, he entered the cave and gathered numerous crystals to enhance his lightsaber during his mission to locate the mysterious and lethal Star Forge. The Jedi Enclave was destroyed and shut down during the Dark Wars that followed Malak's death and the Star Forge's destruction. The Dantooine militia sealed the kinrath caves when the city of Khoonda was founded, preventing access to the valuable crystals. Despite this, the kinrath quickly dug a new tunnel to the surface that was even nearer to the city, resulting in an increase in attacks by the vicious creatures.
During this difficult time for the Jedi Order, the exiled Jedi Meetra Surik entered the cave system in 3951 BBY and killed the kinrath matriarch in order to calm the local kinrath community. While exploring the tunnels, she and her allies came across the Crystal Cave, and with the assistance of Jedi Master Kreia, she was able to sense the imprint Revan had left on the chamber. While there, Surik acquired numerous lightsaber crystals, including a distinctive personal crystal that would prove highly beneficial during her fight against the Sith Triumvirate.
More than three centuries after Revan's visit, a group of Jedi, including Satele Shan, Fortris Gall, and Master Dar'Nala, entered the cave to meet with representatives of the resurgent Sith Empire in the weeks following the momentous Treaty of Coruscant. When Darth Baras and Darth Angral arrived to negotiate, Jedi Shan attacked and refused to negotiate with the Sith. Shan realized during the skirmish that Master Dar'Nala had given in to the dark side of the Force in her efforts to destroy the Sith. Before Shan could step in and assist her former master, the Wookiee mercenary Dalborra killed the Togruta. The Cold War between the Sith and the Galactic Republic would continue for years after they fled the caves.
By the time of the Clone Wars, approximately two millennia after the Cold War, the Order had reestablished some connections with Dantooine and made some visits to the Dantooine Caves. Jax Pavan, a Padawan from the Coruscant Jedi Temple, was one of the Jedi apprentices who traveled during the conflict to obtain a rare Dantooinian crystal for use in his lightsaber.