Like the majority of planets, Dantooine was subject to Rakata rule in the long forgotten history of the galaxy. It wasn't until the Old Sith Wars that the Galactic Republic began the colonization and new history of the planet. Although there was no military presence, the Jedi Order protected the settlers and, around 3,997 BBY (Before the Battle of Yavin), a Jedi training enclave was established by Master Vodo-Siosk Baas. Although Revan is the most famous one who fell to the Dark side, many Jedi who attended the enclave did the same.
Like many former Rakata planets, Dantooine contains several ancient structures. One housed the Star Map, which remained intact by the time of the Jedi Civil War. Revan used the Star Map to locate the great Rakatan artifact called the Star Forge, which allowed him to wage war against the Galactic Republic.
In 3,956 BBY, Revan returned to the enclave to undergo training in an attempt to redeem himself. Soon after Revan completed his training and left the planet, Darth Malak arrived to bombard the enclave and the Rakata ruins. This attack caused the settler farming community to decay; a contributing factor to this decline was the Republic's inability to provide assistance to the remote Dantooine. Until the collapse of the Sith Empire, Dantooine was occupied by the Sith, who executed almost all local leaders.
From 3,956 to 3,951 BBY, settlers began to rebuild their community by constructing the outpost of Khoonda. However, the planet was largely infested by mercenaries and salvagers who terrorized the settlers, while at the same time attempted to pillage the remaining Jedi relics.
In 3,951 BBY, the Republic nearly lost Dantooine to the Exchange, who tried to use Dantooine as an outpost. The Exchange attempted to force the settlers off-world, resulting in several skirmishes that eventually led to the Battle of Dantooine. It wasn't until the Jedi arrived and forced the Exchange off the planet that the Republic finally decided to defend Dantooine.
Shortly after, the Jedi enclave was rebuilt and even housed the Jedi Council until Darth Traya killed the council members. Interestingly enough, underneath the deserted Enclave was a hidden facility where Jedi ran cloning experiments.
According to the Threat of Peace comics, both the Sith and the Republic have military bases on Dantooine.This was the reason for the confrontation between Dar'nala, Satele, and the Sith lords Angral and Baras, as the republic commander on Dantooine refused to retreat. The comic ended with the Republic commander agreeing to leave, leaving the status of Dantooine unknown at the current time.
Since Dantooine previously housed the Jedi enclave and the ruins are mainly still intact, it wouldn't be a stretch to assume that someone could still use the cloning facilities to run experiments. If true, then they could be added to bacta (or kolto) as a lore based justification for how players will be able to return to life after they are defeated in-game. This could be applied to the entire galaxy as it also wouldn't be unlikely that the Sith stole the available research information and copied or perhaps altered what was learned.
The intact Jedi enclave could also be refurbished and returned to use as a Jedi outpost or training ground. Or possibly the Sith took over to use the ruins as an outpost or training ground, as the dark side has caused numerous deaths to those who once inhabited these grounds.
Dantooine always seems to be a site of conflict between those in power and those trying to settle. As such, it would be safe to assume that the remaining settlers were left to their own devices after the Republic withdrew from non-essential worlds. Perhaps the settlers put together a militia in an attempt to protect themselves from the Sith, who may now control the world.
Nothing is completely set in stone when it comes to Dantooine and BioWare is known to surprise everyone with their attention to detail and story. If Dantooine is included as a playable planet for Star Wars: The Old Republic, it will definitely not be one that is easily forgotten. After all, those who played Knights of the Old Republic 1 and/or 2 already spent time on the planet, and their experiences and feelings will only help to shape the story that we all are apart of.