The incident received wide press coverage in Hawaii, in part because of the damage caused to a sensitive coral environment, and also because the stranded ship was within sight of Honolulu off the airport.

Navy investigation found that the grounding was caused by a combination of a misread navigation system, a sleep-deprived commanding officer, broken equipment, and an inexperienced and dysfunctional bridge team.

Port Royal spent time in the Pearl Harbor shipyard for $18 million in scheduled repairs, then departed for the open ocean off Oahu for sea trials at 08:15 on 5 February 2009.

The ship was undergoing her first sea trials following the repairs, including full power, steering, and helicopter flight operation checks.

[3][4][5][6] According to the U.S. Pacific Fleet, the ship ran aground while moving very slowly as she transferred shore-based aviation assessment officials to a smaller boat to take them to shore.

[5][12] Once the raw sewage dumped by the ship had dissipated, divers from the Hawai'i Department of Land and Natural Resources examined the site and discovered that the grounding had damaged the coral reef.

[19] At a cost of $7 million, by 27 June 2009 the divers had collected 5,400 loose coral colonies and reattached them to the reef using cement and plaster of Paris.

In a hearing presided over by Vice Admiral Samuel J. Locklear, commander of the United States Third Fleet, Captain John Carroll was given non-judicial punishment for "dereliction of duty and improper hazarding of a vessel."

In a separate hearing, Rear Admiral Dixon Smith, commander of Navy Region Hawaii and Naval Surface Group Middle Pacific, imposed non-judicial punishment on two other, unnamed Port Royal officers and an enlisted seaman for dereliction of duty and improper hazarding of a vessel.

[2] The U.S. Navy safety investigation into the accident, not intended for public release but which was obtained by the Honolulu Advertiser in July 2009, listed several contributing factors for the grounding.

The factors included a misinterpreted navigation system, a sleep-deprived commanding officer, faulty equipment and an inexperienced and dysfunctional bridge team.

During the small-boat transfer, the cruiser's operations officer took a binocular bearing to the harbor landing from the boat deck and noted the position discrepancy, but was unable to correct the ship's course in time.

[3] The report concluded that in spite of the equipment and navigation systems failures, there were enough working sensors and visual clues to prevent the grounding.

[22] Port Royal left dry dock at Pearl Harbor on 24 September 2009 for final repairs and assessment before being returned to duty.

While in dry dock, technicians from BAE Systems and the Navy replaced the cruiser's sonar dome, reinstalled rudders, and made structural repairs to the ship's tanks, superstructure, and underwater hull.

"This settlement agreement recognizes the State of Hawaii's loss of a natural resource and takes into account the U.S. Navy's unprecedented efforts to restore the reef where USS Port Royal ran aground," said Rear Admiral Timothy Giardina, U.S. Pacific Fleet deputy commander.

Said Smith, commander of Navy Region Hawaii and Naval Surface Group Middle Pacific, of the grounding incident upon the departure of the ship, "I've put it behind me.

"[27] Navy command was said to have lost confidence that the vessel had been restored to seaworthiness, and, because of that, the ship was included on a list of seven cruisers slated for early retirement.