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.
At 2:25 am she ran aground on Tubbataha Reef, about 130 kilometres (70 nmi) south east of Palawan in the Philippines.
About 90 minutes after the grounding, she was seen on park radar at approximately 04:00 hours local time.
At the time of the accident, the ship was travelling from Subic Bay in the Philippines to Indonesia.
The extent of any damage to the reef was unknown, but there was no evidence of fuel leaks.
Philippines officials estimate the damage to the reef at 1,000 square meters.

The second night aground the ship shifted and began taking heavy persistent seas to her port side.
DC2 Jeff Macatangay and MN3 Pekarcik navigated a tangle of machinery and pipes in the ship's bilge while it filled with water to construct shoring on the keel, greatly slowing flooding and bought the ship four hours of available power and communications.
They were awarded the Navy and Marine Corps medal for their actions in the dynamic-hazardous environment.

The next day, 18 January 2013, the U.S. Navy evacuated all 79 crew members from the minesweeper to the USNS Bowditch and MV C Champion.
In recognition of his actions in evacuating the sailors aboard Guardian, Petty Officer Travis Kirckof, a mineman aboard USS Guardian and one of the two assigned Search and Rescue (SAR) swimmers, was awarded the Navy and Marine Corps Medal on 11 April 2014.
Petty Officer Kirckof joined by Petty Officer Nick Martin and Matthew Pekarcik stayed in the shark-infested water for almost five hours to assist his shipmates in the evacuation to the nearby reef, saving at least two lives.

On 19 January 2013, an assessment team deployed to plan and execute the vessel's extraction.
On 20 January 2013, Navy Times reported the ship was taking on water in multiple places and experiencing a slight list to port.

Originally, only the bow section of Guardian rested on the reef, but wave action pushed the entire vessel onto the reef, 20 to 30 metres (66 to 98 ft) from the edge.
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 intended extraction, as well as tugboats and Philippine navy and coast guard vessels.
It was intended for Guardian to be removed from the area by crane ships from Singapore, then be placed on a barge or other ship, since the ship was too damaged to be towed due to multiple hull penetrations.
During the time the cranes traveled from Singapore to the Philippines, preparations were made for the lift.
15,000 gallons of fuel were transferred from the tanks in Guardian to other ships, then refilled with seawater to keep the vessel stable.
Dry food stores and the personal effects of Guardian's crew were removed as well.
Salvage workers reinforced the wood-and-fiberglass hull of the minesweeper with Kevlar lines to mitigate stresses from waves hitting the vessel.
Then, salvage workers from Mobile Diving and Salvage Unit One and Smit Salvage chopped the superstructure and wooden hull of the ship into chunks.

On 29 January 2013, the United States Navy announced the ship would be cut into three sections on the reef prior to removal, resulting in the total loss of the $227 million vessel.
USS Guardian was decommissioned and struck from the Naval Vessel Register on 15 February 2013.
On 27 February 2013, salvage workers disassemble Guardian, a process estimated to take a month.
The bridge deck was removed on 4 March 2013.
On 30 March 2013, the stern section of the ship was lifted off the reef, completing the removal process.

In February 2013, Guardian was replaced with USS Warrior in the 7th Fleet, with the crew of Warrior returning to San Diego, and the crew of Guardian taking over Warrior.

On 8 April 2013, the U.S. Navy turned over digital navigation charts and other evidence and documents and data of Guardian to the Philippine Maritime Casualty Investigating Team (MCIT) and responded to "Technical an
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. At 2:25 am she ran aground on Tubbataha Reef, about 130 kilometres (70 nmi) south east of Palawan in the Philippines. About 90 minutes after the grounding, she was seen on park radar at approximately 04:00 hours local time. At the time of the accident, the ship was travelling from Subic Bay in the Philippines to Indonesia. The extent of any damage to the reef was unknown, but there was no evidence of fuel leaks. Philippines officials estimate the damage to the reef at 1,000 square meters. 
The second night aground the ship shifted and began taking heavy persistent seas to her port side. DC2 Jeff Macatangay and MN3 Pekarcik navigated a tangle of machinery and pipes in the ship's bilge while it filled with water to construct shoring on the keel, greatly slowing flooding and bought the ship four hours of available power and communications. They were awarded the Navy and Marine Corps medal for their actions in the dynamic-hazardous environment.
The next day, 18 January 2013, the U.S. Navy evacuated all 79 crew members from the minesweeper to the USNS Bowditch and MV C Champion. In recognition of his actions in evacuating the sailors aboard Guardian, Petty Officer Travis Kirckof, a mineman aboard USS Guardian and one of the two assigned Search and Rescue (SAR) swimmers, was awarded the Navy and Marine Corps Medal on 11 April 2014. Petty Officer Kirckof joined by Petty Officer Nick Martin and Matthew Pekarcik stayed in the shark-infested water for almost five hours to assist his shipmates in the evacuation to the nearby reef, saving at least two lives.
On 19 January 2013, an assessment team deployed to plan and execute the vessel's extraction. On 20 January 2013, Navy Times reported the ship was taking on water in multiple places and experiencing a slight list to port.
Originally, only the bow section of Guardian rested on the reef, but wave action pushed the entire vessel onto the reef, 20 to 30 metres (66 to 98 ft) from the edge. 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 intended extraction, as well as tugboats and Philippine navy and coast guard vessels. It was intended for Guardian to be removed from the area by crane ships from Singapore, then be placed on a barge or other ship, since the ship was too damaged to be towed due to multiple hull penetrations. During the time the cranes traveled from Singapore to the Philippines, preparations were made for the lift. 15,000 gallons of fuel were transferred from the tanks in Guardian to other ships, then refilled with seawater to keep the vessel stable. Dry food stores and the personal effects of Guardian's crew were removed as well. Salvage workers reinforced the wood-and-fiberglass hull of the minesweeper with Kevlar lines to mitigate stresses from waves hitting the vessel. Then, salvage workers from Mobile Diving and Salvage Unit One and Smit Salvage chopped the superstructure and wooden hull of the ship into chunks.
On 29 January 2013, the United States Navy announced the ship would be cut into three sections on the reef prior to removal, resulting in the total loss of the $227 million vessel. USS Guardian was decommissioned and struck from the Naval Vessel Register on 15 February 2013. On 27 February 2013, salvage workers disassemble Guardian, a process estimated to take a month. The bridge deck was removed on 4 March 2013. On 30 March 2013, the stern section of the ship was lifted off the reef, completing the removal process.
In February 2013, Guardian was replaced with USS Warrior in the 7th Fleet, with the crew of Warrior returning to San Diego, and the crew of Guardian taking over Warrior.
On 8 April 2013, the U.S. Navy turned over digital navigation charts and other evidence and documents and data of Guardian to the Philippine Maritime Casualty Investigating Team (MCIT) and responded to "Technical an
USS Guardian (MCM-5)