He then took part in the Anglo-Egyptian War of 1882 as a sub-lieutenant on the gunboat HMS Mosquito and commanded a landing party at Chalof, for which he was specially commended in despatches and specially promoted to lieutenant the same year.

He was promoted to rear-admiral in 1911 and retired at his own request in 1912, settling in Guelph, Ontario.

On the outbreak of the First World War in 1914, Story offered his services and was appointed Admiral-Superintendent, Esquimalt Dockyard, in the Royal Canadian Navy, as well as Senior Naval Officer West Coast.

In retirement, Story, the only full admiral living in Canada, eventually settled in Montreal, and was involved in various patriotic organisations until his death in 1938.

One daughter, Mary Catherine Story, served in the United States Army during World War I as a telephone operator.