It could just as easily have been a rock.

Instead, what the crew of the submersible Pisces V found on the sea floor off Hawaii in August was a huge Japanese submarine that the United States sent to the bottom of the ocean in 1946, lest it become a Cold War trophy for the Soviet Union.

The submarine, the I-400, was one of five that met a similar fate; some of the others have already been discovered. But Terry Kerby, the longtime operations director and chief submarine pilot for the Hawaii Undersea Research Laboratory, or HURL, called this one “the real prize.”

Besides being the first of its class, it has particular historic value. “This one actually trained for a mission: Attack the Panama Canal,” Mr. Kerby said....