YOKOSUKA, Japan—As most of its crew slept on Friday night, the USS Fitzgerald passed through one of Japan’s busiest shipping lanes just south of Tokyo, a watch crew assigned to guide its passage.

In a period of seconds, a 29,000-ton cargo ship loaded with containers plowed into its right side, crushing a large section of the destroyer’s main structure, including the captain’s cabin and sleeping quarters for 116 sailors below the waterline. Seawater flooded in through a large gash.

As...