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In Level 6:Kadingir Sanctum in the cave where you get the Chaingun there will be a head of a skeleton on a spike wearing a football helmet. The football helmet itself looks very similar to the one Commander Keen wears. Both Doom and Commander Keen were made by ID Software.
Contributed by TheGrayGamer
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The Cyberdemon's theme has hidden pentagrams and 666's that can be viewed in the song's spectrograph.
Contributed by Mass Distraction
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The trophy/achievement "Shoot it Until it Dies" earned after defeating the Cyberdemon boss is a reference to an infamous "pro tip" once created by Doomworld co-founder Andrew "Linguica" Stine as an April Fool's joke that over the years has been mistaken for a genuine scan from an old GamePro magazine.
Contributed by Mass Distraction
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Images leaked from the time the game was still being called Doom 4 show a completely different looking game. The setting seems to have been post-apocalyptic, and some images show soldiers in a broken down city. Not much else is known about this early version.
Contributed by Mass Distraction
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The Cacodemons went through a redesign during the development of the game. They were recolored and slightly altered to look more like their original sprites.
Contributed by Mass Distraction