The story arc is an adaptation of the backstory described in Jedi Apprentice: The Dark Rival, although it follows a very different storyline.
Twenty-one years before the events in Star Wars: Episode I The Phantom Menace, Jedi Master Qui-Gon Jinn is dispatched to prevent the outbreak of a civil war on the homeworld of his Padawan Xanatos—whose father is king. It is a mission that will lead Qui-Gon into close contact with the dark side and start him on a quest that will have a major impact on the future of the Jedi Order!
Many of the characters and places in Jedi—The Dark Side are based on those that originated in Jude Watson's Jedi Apprentice series by Scholastic: Xanatos, Crion, Tahl, Thani, Landor, etc. The story is an expansion on Watson's introduction of the Telosian Civil War and Xanatos' fall to the dark side upon the "murder" of his father Crion by his Jedi Master.
The final issue of Jedi—The Dark Side promises further comics chronicling Qui-Gon Jinn's life before the Jedi Apprentice series, but they never materialized.