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Doom is split up into three chapters, each containing eight missions. The Ultimate Doom, a re-release of the original game, adds a fourth chapter (Thy Flesh Consumed) containing nine new missions. The chapters can be played in any order; this walkthrough begins with the first chapter, Knee-Deep in the Dead.

At the beginning of each chapter you get to select a difficulty level; I'm Too Young To Die makes the enemies weaker and less numerous, while Ultra-Violence and Nightmare fills the levels with difficult foes.