Think of Marka Ragnos as the Emperor Palpatine of 5,000 years before the Galactic Civil War. He was bad news, and after ruling the galaxy with an iron fist (as seen in Dark Horse's Tales of the Jedi: The Golden Age of the Sith), he was the type to always be plotting his return. Even millennia after his death.
That's where 2003's Jedi Knight: Jedi Academy came in. As a pupil of Kyle Katarn, players who chose to follow the light side ended the game by defeating a fallen Academy student possessed by the spirit of Marka Ragnos, who was poised to rule the galaxy again.
Marka Ragnos' legacy was referenced in all three "Old Republic" games as well, most notably BioWare's classic Knights of the Old Republic, where players could view his mummified corpse.