John and his daughter were caught in an accident on the Zakim Bridge in Boston. The water below the bridge turned to blood, and the distraction to the drivers caused an accident, in which John's car was pushed off of the bridge and into the water. John's daughter drowned as a result. John escaped and exhibits some of the symptoms of being in contact with The Presence, however his psychological evaluation and interview do not allude to any direct contact.
John then took the name "John of Boston," and started preaching to people about his "baptism in blood". He was arrested and was released on bail for conducting an unapproved crowd of more than 20 people. While out on bail, he was arrested again for the same crime. The officers allowed him to finish preaching for fear of a riot. He was put into Judson Ogram Correctional Facility for his crime. Dr. Gantry seems to be a possible follower of John as he tries to tell him that if John doesn't publicly repent on his preachings, he will be killed. He showed some sort of interest in Dr. Gantry's partner, Francesca, and it is suggested John is projecting her as a surrogate for his daughter.
His innocence is disregarded, as suggested by police notes on his transfer document, because they want to keep him out of the public eye. John is put onto a high dose (20mg every 10 days) of Flupentixol, an antipsychotic that lasts up to 4 weeks from a single injection. He refused to to sign a rebuttal of his comments with a public statement confirming this action, and is subsequently executed.
- In the conversation between Dr. Gantry and John, John turns Dr. Gantry's wrist over, and Dr. Gantry makes a comment about "Mark of the Beast." Given the recent nerochip developments, this hints that at least Dr. Gantry has a nerochip implanted in him which suggests that has committed a violent crime in the past and may be one reason he is sympathetic towards John.
- As clear as it might be to some, it is worth pointing out the similarities between John of Boston and John the Baptist. Recall that John the Baptist was the prophet that cleared the way for and spoke about the coming of Jesus. John of Boston has been serving a similar role, although more focused on the Presence instead of a human embodiment. Also, John the Baptist drew people to him and his message, much as John of Boston did with the inmates and the people. John the Baptist was, near the end of his life, imprisoned for his speaking out against the rulers of the time, and was eventually beheaded for that act. John of Boston met a similar end, except with a bullet to the head. As a final note, there is a sense of irony that the text hint derived from the background images is tied to Darwin's Origin of Species.
- Although subtle, John's last name appears to be another in the varied references to the research and the physical location Fermilab, an integral Particle Acceleration Lab in Particle, Time and Space research.
- Many speculate that the song Vessel is about John due to the fact that in the transcript of his discussion with the facility member he mentions that he is a vessel for the truth.