Due to the show's cancellation after one season, the final episode ended on an unresolved cliffhanger that revealed Digger, John's close friend, as the leader of the Phoenix Organization.

Series creators Brandon Camp and Mike Thompson revealed in an Entertainment Weekly interview what the planned resolution would have been, since the show was cancelled before it could be resolved on screen.

According to the creators' intended reveal, the villain unmasked in the finale was not actually Digger but a Phoenix Organization member who had undergone facial reconstruction to look like him.

The planned backstory revealed that the Phoenix Organization believed John Doe was a Messiah figure and was actually protecting him from a rival group that wanted him dead.

John Doe's true origin, per the creators' unfilmed plan, was that he had been injured in a boating accident, with the mysterious mark on his chest being a scar from shrapnel caused by the explosion.

The character's encyclopedic knowledge (his 'Überbrain') was intended to be explained as a by-product of transcending his body during a near-death experience, during which he traveled to a spiritual plane where all the universe's questions are answered.

The series holds a score of 65 out of 100 on Metacritic based on 22 reviews, indicating 'generally favorable reviews,' and a 73% approval rating on Rotten Tomatoes based on 26 reviews.

Variety critic Phil Gallo praised the show for Mimi Leder's direction and Dominic Purcell's magnetic lead performance, saying the series 'has a solid identity.'