As of 29 October 2012, Guardian is commanded by Lieutenant Commander Mark A. Rice, and is part of Mine Countermeasures Squadron 7. She is assigned to the 7th Fleet, and forward-deployed to Sasebo, Japan.
On 17 January 2013 following a port call and fuel stop in Subic, Guardian proceeded across the Sulu Sea and entered the Tubbataha Reefs Natural Park.
After appearing on Park radar, at approximately 0400 hours local time Guardian was radioed a warning by park officials that the vessel had entered a restricted area. Park officials claim their lawful warning was met with disregard by Guardian, which radioed back to "bring [their] complaint to the U.S. Embassy." Guardian ran aground on Tubbataha Reef shortly thereafter about 130 kilometres (70 nmi) south east of Palawan in the Philippines. At the time of the accident the ship was travelling from Subic Bay in the Philippines to another port. The extent of any damage to the reef was unknown, but there was no evidence that there was a fuel oil leak. Philippines officials later estimated the damage to the reef at 1,000 square meters. The U.S. Navy evacuated all 79 crew members from the minesweeper to the USNS Bowditch and MV C Champion on 18 January. On 19 January, an assessment team was deployed would plan and execute the vessel's extraction. On 20 January 2013, Navy Times reported the ship is taking on water in multiple places and is experiencing a slight list to port.
It could take two weeks to remove the Guardian from the reef. Guardian now rests about 20 to 30 meters from the edge of the reef. Originally, only its bow was on the reef, but waves have now pushed the entire ship onto it. The guided missile destroyer USS Mustin, the oceanographic survey ship USNS Bowditch and the rescue and salvage ship USNS Salvor arrived in the area to help in the extraction, as well as tugboats and Philippine navy and coast guard vessels, are currently in the area to assist. The Guardian would be removed from the area by crane ships from Singapore to then be placed on a barge or other ship since the ship is too damaged to be towed due to multiple hull penetrations. During the time that the cranes made their journey from Singapore to the Philipines, preparations are being made for the lift. 15,000 gallons of diesel fuel was extracted from the tanks in the Guardian to other ships that were on station and refilled with seawater to keep the vessel stable. Dry food stores and the personal effects of the Guardian's crew were removed as well. Salvage experts have also begun to reinforce the wood-and-fiberglass hull of the minesweeper with Kevlar lines to mitigate stresses from waves hitting the vessel.
On 29 January, 2013, the United States Navy announced that the ship will be cut up on the reef, prior to removal, resulting in the total loss of the ship to the Navy. As a result, the ship will be decommissioned and struck from the Naval Vessel Register in a few days.