The show has been cancelled, the last episode having aired in April, 2003.
More information at:
http://www.tvtome.com/JohnDoe/
It appears there were 21 episodes in all; as American TV series typically run 22 episodes a season, it is possible at least one episode was not shown.
I never saw the show myself, but I remember seeing promos and if I recall correctly, the reviews were good.
That is a problem with American TV now; few shows are allowed to build an audience. If they don't pull in a large audience right away, they are history.
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