The history of the Academy all but ended with the climax of the Jedi Civil War. However, due to the experience and training that the crew had and the sheer power and fighting prowess of the former Dark Lord, they managed to defeat the Sith and escape, killing most of the Sith present at the Academy. Unintentionally revealing his purpose for visiting the tombs, the guards attacked, pitting the entirety of the Academy against the crew of the Ebon Hawk.
When leaving the valley, Revan and his crew were interrogated by the Sith Guards about why he left the Tomb of Naga Sadow untouched during his visit. However, the redemption of Yuthura Ban and the death of Wynn caused an uprising at the Academy. After Wynn's death, Revan convinced Ban to leave the Academy and rejoin the Jedi Order. During this time, Revan killed Wynn with the help of fellow apprentice Yuthura Ban, Wynn's own apprentice. Revan would return to Korriban in the guise of a Sith apprentice and infiltrate the Academy during his search for the lost Rakatan Star Maps.
Unbeknownst to Wynn, Revan had been captured by the Jedi during the war and his memory altered. Jorak Uln was eventually exiled and succeeded by his apprentice Uthar Wynn who operated the Academy during Lord Revan's reign over the Empire. Its students during this time were either Force-sensitives looking to take a side in the conflict, or fallen Jedi, disillusioned with either the Jedi Order, the war, or the Republic in general.
When Darth Revan and Darth Malak reopened the Academy upon their return as Sith Lords to train warriors for their Empire, classes resumed in the sublevels as they trained to fight in the Jedi Civil War. The most likely place to find our lost Jedi is the ruins of the old Academy." ― Kreia, to Meetra Surik īy the time of the Mandalorian Wars, the entrance to the Academy was the only surface level structure remaining, with sublevels being employed for the training of apprentices. " There is much that would draw a Jedi to this place.