Raised in the Edgartown Baptist Church, he declared early on that he wanted to be a Christian. An imaginative youth, he also showed an early penchant for scheming. He was sent to Phillips Academy Andover at age 16 with ministry as his goal and at age 22 graduated from Brown (Baptist) College (now Brown University), in Providence, RI. Once ordained to the Baptist ministry, he enrolled at Newton Theological Institution eventually becoming pastor of a Baptist Church in Middletown, Connecticut. Prescott had married his childhood sweetheart, Betsey Evelyn Phinney, of Edgartown.

During the summer of 1896, Prescott returned with Betsey to Edgartown from Deland, Florida where he had been a minister. While vacationing on the island he fell ill with typhoid fever. He was quarantined for two months, so his wife went to Philadelphia.

As an adult, Prescott wrote: "I used to think those early days on the Roman were mere childish memories, of no great significance for my character. I was wrong. Ninety percent of what I was to become and do settled there. My father was an aristocrat of the sea. From him I learned, wisely or not, to regard myself as the equal in personal worth of any man. Roving too was bred into me; no place has ever seemed thoroughly home to me. The Planet itself merely a port of call. Life has been harder on account of this twist of character, but much more exciting ."

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