The mystery happened on the largest of the Flannan Islands, Eilean Mor, which is part of a group of seven islands, sometimes referred to as The Seven Hunters.
The three lighthouse keepers, Thomas Marshall, James Ducat and Donald McArthur, disappeared on the island without a trace, leaving only speculation behind.
A relief boat was supposed to sail to the island several days before, carrying supplies and a change of crew - but due to the storm this was delayed.
When there was no sign of the keepers at the lighthouse, who should have been waiting at the front of the lighthouse to welcome the boat, a through search of the island and property was made - with nothing out of the ordinary uncovered.
The interior of the lighthouse itself was as should be, with oil in the lamps waiting to be lit and ashes in the grate.
The only thing which appeared out of the ordinary was the two sets of missing oilskins - the outdoor gear the keepers donned.
Only one set remained, belonging to Donald McArthur - meaning he had gone outside in a ferocious storm in just his clothes.
This was not only unheard of, but also illegal. One of the rules of the Northern Lighthouse Board was that one man always must remain inside the lighthouse.
The following investigation carried out concluded that two of the men must have been outside during the storm and were swept away by the waves.
Donald McArthur then ran out to their rescue but was also swept away. But even the official investigation was mere speculation as no proof to this story has ever appeared. It is simply as if the three men walked off the island.
The Scotsman newspaper received a telegraph alerting them of this event, and reported it on Friday 28 December, 1900.
In the original report it was written: “There are four lighthouse men attached to this station. Three of them are always on the rock attending to the light.
“Each of the four in turn is six weeks on the island, and a fortnight on the main land. During that fortnight they reside at the township of Breaselete, on the north side of Loch Rosg.
“The Flannans are visited every fortnight by the Commissioners’ steamer Hesperus and it was on this vessel, which is under the command of Captain Harvey, making her usual call at the lighthouse with stores on Wednesday, that the unfortunate discovery was made that the whole of the lighthouse staff were missing. But for the lighthouse men, these rocky and lonely islands are uninhibited.
“The Hesperus left Oban on Monday and took on board the keeper, who after a fortnight on shore was returning to relieve one of this comrades. On the boat’s crow landing at Eilean Mor, no one was to be seen.
“The tower and the residences of the keeper were searched but none of the men could be found.
“A rocket was fired, but there was no response and the painful convictions was forced home that the lighthouse keepers had been swept off the island and drowned.
“All the clocks in the building were stopped, from which it is considered possible that the disaster occurred at least a week ago - presumably Thursday last, the 20th - the day of the terrific gale which did so much damage all over Scotland, and wrecked part of the Shetland fishing fleet.”