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The lighthouse is located on Eilean Mòr in the Outer Hebrides of the northwest coast of Scotland, on an inhospitable rock in the north Atlantic Ocean. Eilean Mòr is one of seven rocky islands making up the Flannan Isles, also known as the Seven Hunters.
The lighthouse was a typically clever piece of Victorian engineering designed by David Alan Stevenson, first cousin of author Robert Louis Stevenson, and member of the distinguished Stevenson family of lighthouse engineers. It was built from 1895-99 and first put into use on 7 December 1899.
As well as a lighthouse, facilities included a cable-hauled railway and steam engine, used to bring supplies (principally fuel for the lamp) from ships up to the lighthouse.
After the disappearance, things seemed to get back to normal. Facilities were modernised through the 20th century, until the lighthouse was fully automated in 1971 and the keepers went home for good.
On 15 December 1900, the Archtor, a boat travelling from the USA to Scotland, noticed that the lighthouse's light was not burning. This wasn't considered as requiring emergency action. A few days later the lighthouse supply vessel with relief keeper Joseph Moore set out on its routine journey to resupply the lighthouse, after a delayed departure due to bad weather, reaching the island on 26 December.
When he arrived, there was no sign of any of the three experienced keepers meant to be manning the lighthouse, Thomas Marshall, James Ducat, and Donald MacArthur. The door and gate were shut; the lamp was filled but unlit; and there was no sign of any disaster. The only odd things inside were an overturned chair and the fact that one of the three men had left his waterproof oilskins inside the lighthouse; outside there was damage to the railings, the railway, and a box used to store ropes; a large boulder had been moved, and grass ripped out.
The keepers had kept a journal, which reported severe storms on 12 December, though they reportedly had subsided by the time of the last entry on 15 December. The entries showing this were published by an American newspaper, although there have been suggestions that the newspaper made it up.
The most likely explanation is that bad weather was responsible: a large wave or waves could have swept them off, and once in the water it would be almost impossible to get out, with the sea very cold and heavy waves throwing them against the cliffs. The damage seen outside could have been caused by a sufficently large wave. Presumably the men had either all gone out for some task, or following the disappearance of one or two men, his colleague(s) had gone out to investigate and likewise been carried away by the storm.
The official Northern Lighthouse Board investigation following the disaster found that the men had left their post to attempt to secure a box in bad weather or repair some other damage, and a wave had risen 110 ft (34 m) up the side of the rock and swept them off. There were signs of damage 200 ft (60 m) above the sea consistent with high seas. The inquiry also noted that the men were in breach of regulations, because one should have remained at the lighthouse at all times.
Some doubt is thrown on this explanation by the journal entry reporting that the storm had died away by 15 December, and by the experienced keepers' failure to follow regulations, but it's not hard to imagine the storm picking up again or some special circumstances in which the lighthouse was left unmanned.
Another common theory holds that the men had argued, one had killed the other two and then commited suicide in remorse. There wasn't any evidence to support this: the overturned chair didn't indicate a particularly violent struggle.
This was not perhaps as fanciful a theory as it appears: there was a notorious case at Smalls Lighthouse in Wales in 1801 where one of the two keepers had murdered the other in a period where bad weather had prevented any resupply or relief; the killer had reportedly deteriorated physically and mentally in his time alone on the rock.
The early 20th century was a time of considerable paranoia about German spies infiltrating the UK. It has been hypothesised that spies had visited the lighthouse and murdered the keepers for unknown reasons. Alternatively, the keepers could have been captured and taken onboard a boat. There is still the mystery of why one of them left his coat.
Sea monsters and giant birds have been mentioned. Presumably whatever it was came out of the sea or sky, snatched the men, and ate them. This idea has inspired a variety of science fiction (see below), but it's hard to tell if anyone takes it seriously.
It was more fancifully suggested that some supernatural being had killed them, either the Devil himself or the mysterious Phantom of the Seven Hunters. The island was widely perceived as mysterious; it had old associations with early Celtic Christianity, with a Saint Flannan having built a chapel on the island in the 7th century (it's not entirely clear which St Flannan).
The incident is perhaps best known from Wilfrid Wilson Gibson's poem Flannan Isle (1912). The poem tells the story of a ship sent to investigate the unilluminated light. Filled with foreboding and imagining they smell "some strange scent of death", the rescue party enters the lighthouse to find the table spread with food for dinner and an upturned chair on the floor; a starving pet bird cheeps plaintively. The men search the lighthouse and find nothing.
Gibson invented several details. One of its false claims was that the keepers left their dinners uneaten on the table when they ran out and disappeared; the same untruth is also found in Arthur Conan Doyle's erroneous 1884 account of the mystery of the Marie Celeste (as he called it; it was actually the Mary Celeste). Gibson poetically imagines three living men setting out to relieve the three dead men, which is a little neater than what happened in real life; Moore's arrival is not accurately described. Most incorrectly, the poem claims that there was a long history of mysterious happenings at the lighthouse, including six keepers dying suddenly, three going mad, and one committing suicide by jumping off the lighthouse tower; as already mentioned, the lighthouse had only opened the year before, and no such horrors took place.
Other fictional representations
Fictions and artistic works more or less inspired by the incident include:
- "Horror of Fang Rock", a 1977 Doctor Who story. The Fourth Doctor (Tom Baker - the one with the scarf and curly hair) visits a lighthouse off the south coast of England in the early 20th century and finds one dead keeper and two alive but scared ones dealing with strange happenings. The villain turns out to be a shape-shifting alien called a Rutan. The Doctor even quotes from the poem at the end of the serial, reciting 'Aye: though we hunted high and low/And hunted everywhere/Of the three men's fate we found no trace/Of any kind in any place/But a door ajar, and an untouched meal/And an overtoppled chair.' as he and his companion leave the now-deserted island. 
- Peter Maxwell Davies's chamber opera The Lighthouse. The lighthouse keepers bicker and become convinced a strange beast lurks in the fog; it's all very mysterious and suggestive.
- An early song by prog rockers Genesis, "The Mystery of Flannan Isle Lighthouse".
- Dyatlov Pass, a similar case, where people apparently rushed out into a harsh winter and died.
- Flannan Isles, Northern Lighthouse Board website
- Missing lighthouse keepers remembered after 100 years, The Telegraph, 2000
- See the Wikipedia article on Flannan Isles Lighthouse.
- The 115-Year-Old Mystery of Flannan Lighthouse's Missing Keepers, Mental Floss
- The Curious Disappearance of the Eilean Mor Lighthouse Keepers – A Scottish Mystery, ancient-origins.net
- A Rock and a Hard Place: Storms, Death and Madness at the Smalls Lighthouse, Trinity House of Deptford Strond, 2013
- Lighthouses: a Mystery and a Tragedy, Ana The Imp, 2009
- Flannan Isle, Wilfrid Wilson Gibson, Poem of the Week
- See the Wikipedia article on Horror of Fang Rock.
- The Lighthouse, maxopus