Construction, between 1895 and 1899, was undertaken by George Lawson of Rutherglen at a cost of £1,899 (equivalent to £277,066 in 2023) inclusive of the building, landing places, stairs, and railway tracks.

The railway was removed, leaving behind the concrete bed on which it had been laid to serve as a roadway for a "Gnat" – a three-wheeled, rubber-tyred cross-country vehicle powered by a 400-cubic-centimetre (24 cu in) four-stroke engine, built by Aimers McLean of Galashiels.

[9] The first record[3] that something was abnormal on the Flannan Isles was on 15 December 1900 when the steamer Archtor, on a passage from Philadelphia to Leith, noted in its log that the light was not operational in poor weather conditions.

Jim Harvie, the captain of Hesperus, attempted to reach them by blowing the ship's whistle and firing a flare but was unsuccessful.

He found the entrance gate to the compound and the main door both closed, the beds unmade and the clock unwound.

Captain Harvie sent a telegram to the Northern Lighthouse Board dated 26 December 1900, stating: A dreadful accident has happened at the Flannans.

[14] On 29 December 1900 Robert Muirhead, a Northern Lighthouse Board (NLB) superintendent, arrived to conduct the official investigation into the incident.

[19] No bodies were ever found, but there have been some mysterious sights resulting in "fascinated national speculation" in newspapers and periodicals of the era.

[20] Implausible stories ensued, such as that a sea serpent had carried the men away; that they had arranged for a ship to take them away and start new lives; that they had been abducted by foreign spies; or that they had met their fate through the malevolent presence of a boat filled with ghosts (the baleful influence of the "Phantom of the Seven Hunters" was widely suspected locally).

The 1912 ballad "Flannan Isle" by Wilfrid Wilson Gibson refers erroneously to an overturned chair and uneaten meal laid out on the table, indicating that the keepers had been suddenly disturbed.

[17] Yet, as we crowded through the door, We only saw a table spread For dinner, meat, and cheese and bread; But, all untouch'd; and no-one there, As though, when they sat down to eat, Ere they could even taste, Alarm had come, and they in haste Had risen and left the bread and meat, For at the table head a chair Lay tumbled on the floor.

[21] However, in a first-hand account made by Moore, the relief keeper, he stated that: "The kitchen utensils were all very clean, which is a sign that it must be after dinner some time they left.

This was also puzzling, as all three men were experienced lighthouse keepers who knew they were in a secure structure 150 feet above sea level and should have known they were safe inside.

It was possible McArthur saw a series of large waves approaching the island and, knowing the likely danger to his colleagues, ran down to warn them only to be washed away as well in the violent swell.

[23] Recent research by James Love discovered that Marshall was previously fined five shillings when his equipment was washed away during a huge gale.

Allegedly, McArthur was a volatile character; this may have led to a fight breaking out near the cliff edge by the West Landing that caused all three men to fall to their deaths.