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.
When a young Seattle DJ is mysteriously murdered by a seemingly non-existent perpetrator, Doe helps unravel the enigma while pursuing a relationship with Rachel Pembroke (from 'Manifest Destiny').
The mysterious symbol on Doe's chest is part of the calling card left by a serial killer known as The Mourner who knows a lot about Doe, whom he challenges with cryptic clues as he puts more lives in danger.
John boards a flight for London but discovers a murder-mystery in mid-air while getting to know a pretty fellow passenger and neurologist.
John discovers clues that lead to his real life, a trail that takes him to Idaho and raises more questions than answers.
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.
Investigating a violent and seemingly impossible crime committed at the Seattle Museum of Art, John discovers that Karen is involved.
Doe suspects a link to his own identity when a naked man with a similar brand and no recollection of who he is washes ashore from Horseshoe Island, similar to Doe's arrival in town.
When skeletal remains are found at a construction site, the ownership is traced to a man who is a dead ringer for John.