[Closed] SPOILER ALERT: john doe
I think John Doe might be Windom Earle's body!
Bobby seems clear his dad died in a fire, and that his mom mentioned Cooper ( actually "Mr. C." ) visited Briggs not long before that happened.
Given Mr. C's possession of Major Brigg's military equipment, and their meeting shortly before his disappearance, it's a safe bet.
My bet is on Briggs too.