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The show John Doe from 2002/2003 was cancelled before we found out who John was or where he came from. Does anyone know more about that? John was such an interesting character -- had amnesia, could only see black and white, had access to the sum of human knowledge (like the number of dimples on a golf ball).

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From Wikipedia, derived from an interview with the series creators in Entertainment Weekly:

Due to the series' cancellation, the final episode ended with an unresolved cliffhanger, revealing that Digger, John's close friend, was in fact the true leader of the Phoenix Organization. In an interview with Entertainment Weekly, series creators Brandon Camp and Mike Thompson revealed what would have happened and John Doe's true identity.

"Make that someone who looked like John's friend. The villain unmasked in the finale was actually just a Phoenix member with some fancy facial reconstruction. Turns out, the Phoenix believed Doe was the Messiah and its members were actually protecting Doe from a second group, which wanted him dead. The truth: Doe was injured in a boating accident. That mark on his chest? A scar left by a piece of shrapnel from the explosion. His Überbrain? A by-product of transcending his body during a near-death experience, traveling to a spiritual plane where all the universe's questions are answered."

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Thank you!! And let me just say, that's a pretty EPIC backstory for the character! I sure wish they'd continued with the series, because that premise has so much potential for great storylines!!! –  BrettFromLA Jul 1 at 19:38
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In an interview (2006) Dominic Purcell, the actor who played the titular character, had this to say:

Apparently I was the messiah returned.

[The Pheonix group] were working for the Vatican. ... The Catholics. They didn't want it to be revealed that the true Christ had returned.


From another interview (2007) with the actor:

Well, John Doe was Christ returned. That’s why he knew everything,...

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I do wonder why he was color blind (although, there were things he could see in color). –  Oliver_C Jul 1 at 21:33
    
Awesome! Thanks! I gave you an up-vote, but I can only mark one of the answers as The Answer (with that green checkmark) so that's all I can do. –  BrettFromLA Jul 1 at 23:17
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