In 1941 she was with the maintenance reserve at Rosyth, but in August was part of the Royal Navy's escort flotilla with convoy FS559 when she ran aground, becoming a total loss, on Haisborough Sands[1] on 6 August with a loss of sixteen crewmen.

On 5 August Convoy FS 559 was proceeding down the East coast of Britain to London from Newcastle.

By the early hours and daylight of 6 August, the convoy was enveloped in a thick sea mist, making visibility very poor.

It is thought that due to the combination of the bad weather conditions, the strong westerly drift, and the fact that the exact position of the convoy was unavailable, HM Agate led seven of the convoy's ships onto the sands, where they ran aground.

[4] All three officers of Agate were lost; eight men survived, five of them picked up from a Carley raft by HM Trawler Basset.