When skeletal remains are found at a construction site, the ownership is traced to a man who is a dead ringer for John.

When a young boy Wesley and his mother approach John Doe claiming that sperm bank records indicate he is the boy's father, John is pulled into a mystery as he tries to track down the list of donors and finds two of them dead, their brains removed.

The case of a mysteriously kidnapped teenage girl sends John Doe and Det. Frank Hayes on a frantic investigation to save her before it is too late.