John Doe doesn't know who he is. In actuality he's part of a top-secret government experiment in genetic engineering and/or cloning (codenamed Phoenix) and somehow either escaped or was lost by accident.... One mystery ultimately leads to another, and so on and so forth, until the final episode which makes absolutely no sense and is a huge anti-climax for the audience.
Sounds like the plot for "The Pretender" and about 10 other shows, so you're probably safe assuming that.