In Doom 3, Doomguy appears similar to his classic Doom incarnation, with the exception that his facial features are not concealed, since he does not wear a helmet (even though all other marines in the game wear the same helmet as the original Doomguy).
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In the Doom 3 novels his name is John Kane (who has the same last name as Quake 4 protagonist Matthew Kane).
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In Doom 3: Resurrection of Evil, the main character is different from the Doomguy of Doom 3.