[1] The ship, captained by Hisao Ōnishi, headed for Hawaii on a planned 74-day voyage to train high school students who were interested in pursuing careers as fishermen.

[2] On 9 February, USS Greeneville, a U.S. Navy nuclear-powered attack submarine, prepared to depart Pearl Harbor, Hawaii, to perform a public relations mission as part of the USN's Distinguished Visitor Embarkation (DVE) program.

[4] Accompanying the DV civilians on the mission was Navy Captain Robert L. Brandhuber, Chief of Staff for Rear Admiral Albert H. Konetzni Jr., the commander of the submarine component of the United States Pacific Fleet, abbreviated as COMSUBPAC.

A few minutes later, they detected a second vessel estimated to be about 20 nautical miles (37 km) away (submarine passive sonar does not give range (distance) information), which was designated as "Sierra 13" (S-13).

[12] Before beginning the maneuvers, Waddle checked the submarine's sonar contacts and noted that there were several surface vessels in the vicinity, but none closer than seven nautical miles (13 km) away.

Because Greeneville had not maintained a steady, slow course for a sufficient amount of time, the sonar data available to the Fire Control Technician of the Watch FT1 (SS) Patrick Seacrest did not allow accurate determination on Ehime Maru's range or course.

[19] Also, due to time constraints ordered by Waddle, the ship did not perform normal maneuvers which would be used to obtain accurate course and range information on the sonar contacts prior to proceeding to periscope depth.

Lieutenant, Junior Grade Michael J. Coen, the officer of the deck, conducted an initial low magnification periscope search of the area and sighted no ships nearby.

Waddle, however, aware that they were still behind schedule, conducted a short scan, searching primarily in the sector where he believed the known contacts were located,[20] noted that the haze was still present, and saw no ships in the vicinity.

As the heavy, partially submerged submarine bobbed in the ocean, it also displaced large waves that, in Waddle's opinion, threatened to capsize the life rafts in which Ehime Maru's survivors were gathering.

[32][33] On 11 February, during an "extremely emotional exchange", the commander of the U.S. Pacific Fleet, Admiral Thomas B. Fargo, personally apologized to families of the Ehime Maru's victims, who had arrived in Hawaii the day before.

"[38] In February 2001, vice chief of naval operations Admiral William Fallon was given Presidential special envoy status and dispatched to Japan to apologize for the collision.

[40] His deferential show of contrition to the families, performed in front of news cameras, was widely credited with ameliorating a situation that had the potential to damage US-Japan relations.

[51] Rear Admiral Albert H. Konetzni testified during the inquiry that Waddle and his crew had rushed into Greeneville's final maneuvers without taking enough time to ensure that no other vessels were in the vicinity.

Waddle stated later that he felt he needed to testify because he had promised some of the Ehime Maru family members that he would do so, he had heard that Greeneville's crew expected him to, and he wanted to get his side of the story into the record.

[55] The court made several findings, including that Waddle failed to take positive action in response to the non-availability of the AVSDU, nine of the 13 watchstations in and around the control room were manned by substitute personnel, and that one of the sonar operators was unqualified to stand watch.

[56] The court also issued numerous opinions, including that the accident was caused by "a series and combination of individual negligence(s) onboard Greeneville," "artificial urgency" by Waddle to rush the submarine through its demonstration schedule as it began to run late, failure to follow standard procedures, the abbreviated periscope search, distractions and obstruction caused by the presence of the civilian guests, crew training deficiencies, overconfidence and complacency, and Waddle's not paying enough attention to ship contact information.

Instead, the court recommended non-judicial punishment for Waddle and Seacrest and administrative action for Brandhuber, Pfeifer, Coen, Greeneville's chief of the boat MMCM/SS Douglas Coffman, and sonar supervisor STS1/SS Edward McGiboney.

[60] Coen also received an admiral's mast in which he was "counseled for failing to execute his duties to ensure the safe navigation of the ship and to properly supervise watch personnel in the control room".

[61] After 10 months of unemployment, Waddle worked as a project manager for an energy company in North Carolina and, in July 2004, started his own business as a consultant, executive coach, and public speaker.

[63] On 16 February 2001, the USN Supervisor of Salvage and Diving (SUPSALV) and Submarine Development Squadron 5 (SUBDEVRON 5), using the Scorpio remotely piloted underwater vehicle (ROV), located Ehime Maru in 2,000 feet (610 m) of water on the ocean bottom (21°04.95′N 157°49.58′W / 21.08250°N 157.82633°W / 21.08250; -157.82633).

During the next two weeks, the USN used the Scorpio and the Deep Drone ROVs to search the ocean bottom around Ehime Maru for the remains of any of its missing crewmembers, without success.

The USN contracted the Dutch company Smit International[65] and Crowley Maritime Corp., headquartered in Washington state, to salvage the wreck of Ehime Maru.

[66] Using the Phoenix III ROV, contractors, beginning on 20 July 2001, first removed Ehime Maru's mast and other items on the ship's decks that could interfere with the lifting operation.

Assisted by technical experts from Japan, including one from the company that built Ehime Maru, the Rockwater II contract diving support vessel prepared the ship for lifting beginning the first week of August.

Working in low- to zero-visibility conditions, 66 MDSU-1 and 30 Japanese JMSDF divers from the submarine rescue ship JS Chihaya conducted 526 dives over 29 days, searching the wreck.

The divers recovered the bodies of eight of the nine missing people (three crewmembers, four students, and the two teachers), many personal effects, and several items unique to the ship, such as its nameplate, bell, anchors, and helm.

On 15 December, Waddle visited the Ehime Maru memorial at Uwajima Fisheries High School and placed a wreath of white lilies before a monument to the dead, bowed in silence and then read the victims' names aloud.

[76] After the sinking of Ehime Maru, many Japanese people, including government officials, questioned why civilians were allowed in Greeneville's control room during maneuvers that could place other, uninvolved, vessels at risk.

Although the United States and Japan have been strong allies since the end of World War II, the accident involving Ehime Maru showed that the relationship is not always completely harmonious, especially with regard to incidents in which U.S. military personnel or assets injure or kill Japanese citizens or damage their property.