The question that changed Michael Izbicki’s life appeared on a psychological exam he took not long after graduating in 2008 near the top of his class at the United States Naval Academy: If given the order, would he launch a missile carrying a nuclear warhead?

Ensign Izbicki said he would not — and his reply set in motion a two-year personal journey and legal battle that ended on Tuesday, when the Navy confirmed that he had been discharged from the service as a conscientious objector.

In the process, Mr. Izbicki, 25, went from Navy midshipman in the nuclear submarine fleet here, studying kill ratios, to resident of a small Quaker peace community a few blocks from the Thames River, where he prays several times a day, studies Hebrew and helps with the organic garden.

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