We cannot speak of its loneliness, but it must be Britain's most solitary animal. For the last 16 years, every winter, a male greater mouse-eared bat has taken up residence 300 metres inside a disused and exceedingly damp railway tunnel in West Sussex. The greater mouse-eared bat has been all but extinct in this country for decades. This is the only remaining one we know of. The future of the species in Britain appears to rest with one long-lived and very distinctive individual.

The greater mouse-eared bat is so large that observers who first discovered it in Britain likened one to a young rabbit hanging from a wall. In flight, its wings can stretch to nearly half a metre - an astonishing spectacle in a land where bats are generally closer to the size of the rodent that inspired their old name: flittermouse.

The bat has large, mouse-like ears and its feeding habits are as striking as its size. Rather than zig-zagging through darkening skies collecting flying insects, like most bats, Myotis myotis descends earthwards, flapping its wings very slowly as it covers the ground, picking up grasshoppers, crickets, dung beetles and other flightless insects as it goes. Often, it will flop on to the ground, wings outstretched to fold over its prey.

The solitary individual who spends the winters in West Sussex has never been observed in flight. Where it goes each spring is not known, and what it does is not known, nor which other animals, if any, it encounters. All that is known is that each winter the bat faithfully returns to its dark tunnel, where it hangs, almost motionless, for five months. This place of winter rest is a closely guarded secret, for the bat's select band of self-appointed guardians are adamant: there can be no repeat of the scenes of 1957. That year, a live colony had been found inside an old mine on the Isle of Purbeck in Dorset. Although a reasonably familiar sight in southern Europe, where large colonies roost in caves, this was the first time a greater mouse-eared bat had been found in Britain. The Times published photographs, and a media frenzy ensued. Several animals were whisked out of hibernation and transported to TV and photographic studios and filmed for weeks before being returned to their hibernation hole. Disturbing bats mid-hibernation can kill them. Money was also offered for dead specimens and collectors spirited individuals away.

This fascination was fatal: the greater mouse-eared bat was barely seen again in Dorset, apart from reports of "very large, broad-winged bats" in an appropriately gothic setting: flying around Corfe Castle. Although another small colony of greater mouse-eared bats was found in West Sussex in the late 1960s, by 1992 the species was declared extinct in Britain, the first mammal to disappear from our shores since the wolf 250 years ago.

Bats fly beneath our radar. While butterfly sightings have been collected for 400 years and birds have been scientifically monitored for more than 70 years, bats only been systematically counted for less than two decades. Little is known about many of Britain's 18 bat species, some of which exist in perilously low numbers. Today they are threatened perhaps more than they've ever been by the loss of their insect prey, the conversion of old barns and derelict buildings in which they roost, and the bright lights of new suburbs, wind farms and speeding vehicles that bamboozle or kill them.

The unexpected reappearance of the greater mouse-eared bat in its West Sussex tunnel, in 2002, was a symbol of hope. Against the odds, bats are surviving in our human-dominated land and, perhaps more than any other wild animal, they are constantly surprising us.

Bats are great survivors. The oldest known fossil of a bat, found in a quarry in Wyoming in 2003, is about 52.5m years old. Bats have been evolving for so long, and with so many specialised attributes, from echolocation to drastically extended forelimbs, that the order of Chiroptera - "winged hands" in Latin - accounts for one in five species of mammal. They are supremely successful animals. As one expert puts it: when you have been evolving for so long, you've perfected the business of being a bat.

That business is becoming tricker in a human-dominated world. In older times, they were feared and despised. Modern people may be more tolerant, but even beneficent parts of society - from harvesters of renewable energy to vicars - are often hostile to bats. Energy-efficient homes seal up roof spaces where bats once roosted. New roads - and the planned route of the HS2 railway - block traditional foraging routes. LED lighting is particularly disturbing for bats. Wind farms chop them up: according to a study published in 2016, researchers using sniffer dogs to find and retrieve bat carcasses calculated that 29 onshore windfarms killed 194 dead bats per month - a kill-rate that would dispatch 80,000 bats a year across Britain, without accounting for migrating bats taken out by the rapidly expanding rows of offshore turbines.

A greater mouse-eared bat

A greater mouse-eared bat in flight. Photograph: Alamy

Earlier this year, members of the House of Lords spoke in favour of a bill that seeks to remove bats' legal protection in churches unless there is a "significant" adverse impact on rare bat populations. The Bishop of Norwich blamed barn conversions for driving bats into churches, with more than half of 12,000 listed churches housing roosts of bats. Worshippers had "come to the end of their tether," warned the bishop, because of bat droppings despoiling brasses, fabrics and fittings. For much of the 1990s and early 2000s, the Movement Against Bats in Churches - founded by a vicar's wife - campaigned to eliminate the blight of bats. Is there another animal in Britain that has a dedicated protest movement against it?

Bats that overcome these challenges can live a long time. Only 19 mammal species are longer-lived relative to their body size than humans, and all but one of these are bats. (The other is the naked mole rat.) And of these unusually durable mammals, the greater mouse-eared bat is one of the longest-lived of all: it can clock up more than 35 years. Scientists recently discovered that its longevity is probably due to the fact that, unlike most mammals, its telomeres - a string-like material at the end of its chromosomes - do not shorten with age. They hope further insights from the unique biology of Myotis myotis may one day help humans live longer.

Time passes in a different way for such a long-lived animal, and so it seems with its guardians. I first contacted natural scientist and bat expert Tony Hutson in early 2017, and it was more than a year before he agreed to take me to see the bat. Hutson, a retired entomologist from the Natural History Museum, is wary of any interference in the creature's peaceful existence. Each month of winter, Hutson and other local recorders count the bats hibernating in several old railway tunnels, and each month I begged to be allowed to tag along. After the bat was inspected without me in December, January and February, finally Hutson agreed that I could accompany them on an extra trip they would undertake in March, with a big caveat: they didn't normally inspect the bat so late in winter, and could not guarantee it would still be hanging there.

Hutson is the second in a short lineage of champions of the greater mouse-eared bat. The first was a wildlife-loving tea-planter from Ceylon called Captain William Watt Addison Phillips. Phillips grew up in Staffordshire during the reign of Queen Victoria, and headed to Colombo to become a tea-planter when he was 19. Living among the civets, leopards and sloth bears of Ceylon, he catalogued its natural history and published papers including "On the habits of the Ceylon Gerbil".

After retiring, Phillips conducted a survey of the flora and fauna of the Maldives for the Natural History Museum before settling in Bognor Regis in 1959, just after the first greater mouse-eared bat frenzy. Phillips remained active and insatiably curious in retirement, taking an interest in every kind of animal and plant around him. He was also lucky: one day he found a grey long-eared bat - Britain's second-rarest species - sprawled on his dustbin. It was dead. Some years later, Phillips explored some derelict railway tunnels in Sussex with his grandson. In one, they were delighted to discover a small colony of greater mouse-eared bats. Bearing in mind the old shooting aficionado's adage, "What hits is history, what's missed is mystery," Phillips shouldered his gun, brought down a couple and donated the specimens to the eager curators of the Natural History Museum, who added them to their collections.

At the time, Tony Hutson was working as a scientific researcher in the museum and, by chance, had already met Bill Phillips a few years earlier, during an expedition to the Maldives. Hutson had first become fascinated by bats as a boy, when he saw them above an old priory. He was particularly gripped when he first witnessed the mystery of their motionless hibernation. "That got me - that they will sit there without moving for three or four months," he says. "How are they doing nothing?" Growing up in south London, he joined a natural history youth group that met at the Natural History Museum; as a young man, he applied for a job there. He had a cup of tea with a secretary and asked if he could help its scientists who were studying bats. "They said: 'No, but we can give you a job in entomology.'" So Hutson cunningly pursued his passion by studying the ectoparasites - such as fleas - that live on bats.

As one of the museum's bat experts, Hutson spent much of his time coaxing irate homeowners not to destroy colonies of rare bats roosting in their roofs. But there were moments of adventure, too. He undertook an expedition to a cave in Ecuador with Erich von Däniken, the Swiss author of Chariots of the Gods, who believed that aliens visited Earth and influenced early human culture. The explorers were winched into the cave by helicopter and the astronaut Neil Armstrong came along. "The theory was that if we did meet any aliens, he would be the best person for them to talk to," said Hutson. He found no aliens, but they did come across a few interesting bat species.

Tony Hutson hunting for bats in a disused railway tunnel in Sussex.

Tony Hutson hunting for bats in a disused railway tunnel in Sussex. Photograph: David Levene for the Guardian

After taking note of Bill Phillips' surprising discovery of a colony of greater mouse-eared bats in Sussex, Hutson first visited the old railway tunnels in 1974, and saw the bats for himself. "I was working with ectoparasites of bats at the time, so I'd sometimes come down and poke a few around, searching for parasites," he said. The tunnel was bricked up, with a locked door at one end, to stop visitors from causing a repeat of the scenes that destroyed the Dorset population in the 1950s. (The bats gained access via ventilation grills.) Each year in the 1980s, Hutson unlocked the door and counted the greater mouse-eared bats inside. Each year, their numbers dwindled. The Wildlife and Countryside Act of 1981 gave bats and their roosts legal protection for the first time, but then, disaster: one winter, all the female greater mouse-eared bats disappeared from the tunnel. It seemed that their maternity roost - the barn or some other unknown place in Britain where the females raised their young during the summer - must have been destroyed, perhaps in a fire, or by developers. By 1992, the greater mouse-eared bat was declared extinct.

But Tony Hutson did not give up. Each winter, he continued to check tunnels and disused mines all over the south of England. Nine years later, his vigilance was vindicated. He heard reports of a live bat found, grounded, in Bognor, and raced to the seaside town. By the time he arrived, this old female bat had died. And it presented another puzzle: it was disabled.

"A bat's forearms are usually the same length, but on this bat they were different lengths," he remembered. "Whether it spent its life flying around in circles, I'm not sure." Was there a secret, residual population of mouse-eared bats? It appeared not, for this venerable female showed no sign of ever having bred, and no sign of having communed with any other mouse-eared bats. "There were no parasites on it that it would have picked up from others of its kind, which is what I was looking for," said Hutson. But the find put him on high alert.

At the end of 2002, his annual inspection of the old tunnel where the bats had been found by Captain Bill Phillips in the 1960s revealed a single greater mouse-eared bat. It was a young male, born that spring. Hutson and the protectors placed a silver tag on its elbow and wondered how this species would surprise them next.

By March, I was desperate to see this bat. I met Hutson on a murky day in a layby close to the secret tunnel. He had been visiting the bat each month over winter, but offered no crumb of comfort. "Whether he flew off last night, I don't know," he said with a twitch of deadpan humour. We set off through a woodland with some fellow bat enthusiasts: Crispin Scott of the National Trust, and Sue Harris and Martin Phillis, volunteer bat recorders for Sussex bat group and part of a network of bat fans who form the Bat Conservation Trust. This small charity is the national voice for bats in Britain, and Hutson revealed, with characteristic modesty, that he helped set it up.

We walked down the cutting of an old railway line, sharp lumps of chalk and fallen trees tumbling down the banks. The tiniest trace of people having walked along the cutting worried the protectors. "It's too open," said Scott. "We need to fell a couple of trees across here so only people in the know come down." At the end was a tunnel of red brick, marching into the hillside.

At the centre of its bricked-up entrance was an iron hatch. Phillis pulled out a key, unlocked the top and the bottom, and we squeezed inside. The tunnel was cool but not freezing; dark but not pitch-black. Daylight shone from the grille above our heads and in the far distance, like a mirage, was a crescent of light, another grille, 680 metres away, at the tunnel's end.

I hadn't anticipated the water. There was the sound of constant dripping as water oozed through the brick ceiling and hit the stony floor. The bricks glistened with moisture. "Bats need it very humid," said Hutson. "If it gets too dry, they dehydrate." There were black stains on curved tunnel walls and ceiling. Only when we later emerged and discovered our faces were streaked with black did I realise that this was archeological soot, from the steam trains that last entered this tunnel in the 1950s.

The bat protectors wielded head and hand torches and began by painstakingly sweeping their beams up and down the curved walls of the tunnel, inspecting ginger-coloured fungi, straggly like beards, and searching for the bats that clung in crevices where mortar or brickwork had come away. Different species shared this tunnel. Smaller species may temporarily wake from hibernation to pee or feed if it is mild, but the greater mouse-eared goes deeper into the tunnel and remains motionless for longer. Hutson pointed out the different species, with their distinctive features. The natterer's bat has long, trumpety ears and a Daz-white belly; Daubenton's bat has big feet, which it uses to grab insects off the surface of ponds. These bats are counted three times each winter for Bat Conservation Trust hibernation surveys.

We probably didn't need to, but we talked in low murmurs. I walked past the bats' somnolent bodies with the same care I take while tiptoeing into my children's bedroom when they are sleeping.

The first question Hutson asked when he found the mouse-eared bat in 2002 was: where did it go after its winter hibernation? Answer this question, and he might find other members of its tribe. Hutson contacted colleagues in Portugal who better knew its lifestyle and were familiar with its preferred summer habitats. "We organised a big survey, well sort of," he said. "We met in the pub and looked at prime local habitat. It was a time when they were cutting a lot of hay and these bats often go for freshly cut hay, where they can find more insects."

During summer, the greater mouse-eared bat roosts high in church and castle turrets in northern Europe, and in caves in the south. Hutson looked in old sand and chalk mines, and in disused lime kilns. He asked industrial archeologists and consulted other societies for secretive enthusiasts. "There's always some nut looking for holes in the ground," he said. "We combed the region for suitable sites." The bat group appealed to the media, encouraging people to look for big bats. They collected a hair sample to use DNA to identify its origin, but the lab scientists weren't able to extract DNA at the time.

The broadcaster and naturalist Chris Packham came to film the hunt. But there was no trace of the bat or any of its kin. The bat did turn up at the Sussex tunnel the next winter, however, and the winter after that. Hutson considered putting a VHS radio tag on the bat, but was worried that the burden of a tag could kill it, and he would be blamed. "What put me off in the end was if it didn't turn up again that winter, I'd be drummed out of the country," he said. In 2007, however, the protectors plucked up the courage to carefully take the bat off the tunnel wall during its hibernation and inspect it. Its teeth were a bit worn, but it was in good health - and very alone. During his inspection of its private parts, Hutson found signs that it had never been sexually active.

We were now 300 metres inside the tunnel. A natterer's was stuffed into a crevice no wider than a centimetre. "He's awake, isn't he?" said Hutson, swiftly moving his torch away so as not to disturb it. Then he pointed his torch towards a bat that was noticeably larger than the others: solid, and tea-cup sized. "A very rare bat," he said, "but not rare enough for you." A Bechstein's bat.

What of the mouse-eared bat? "He has definitely moved," said Sue Harris, who had noted his position during their previous inspection, in February. We were in the relatively warm middle of the tunnel, where it was 8.2C, but there was no bat. Harris walked ahead. Suddenly, her methodical movements became frantic. "I can hardly contain my excitement," she called out.

Britain's last known greater mouse-eared bat, hibernating in a tunnel in Sussex.

Britain's last known greater mouse-eared bat, hibernating in a tunnel in Sussex. Photograph: Martyn Phillis

High up, where a whole brick had fallen from the curve of the tunnel wall, hung a large, sandy-coloured bat. A silver ring wrapped around its forearm shone in our torchlight. The greater mouse-eared bat. The natterer's bats we had seen weighed 8g. This one weighed more than 30g, with a broad pink muzzle, a long, pale underside, and dark-brown wings folded up tight by its side like an umbrella.

It would be hard to bond with a creature you only ever saw perfectly still, in a deep sleep, face averted from the world. Was Hutson fond of it? "I shall be sorry when it's not there, assuming I outlive it," he said. "You never know - it might have another 20 years to go. It might be having an easy time, no stresses. It looks quite tough, sort of robust." But Harris was worried. "He's looking damp, especially around the neck area. He didn't look at all damp in February," she said. Droplets of water glistened silver on his fur. His ring looked tarnished.

The bat's unknowability was frustrating but, after 16 years, Hutson had become resigned to the unanswered questions about this individual, and the fate of the species in Britain. Where does this bat go? Perhaps to France? Are there really no others? "After a few years I wondered if we should have done more in terms of finding others," said Hutson, "but now I'm convinced it is a loner and whatever we had done wouldn't have made a difference." Could they reintroduce the species using wild specimens caught in continental Europe? "The first problem is that they would have to go into quarantine for at least six months because of rabies. After being in captivity for six months they wouldn't be too good at operating in the wild."

We reached the end of the tunnel. There was no exit, just a solid wall of breezeblocks. The bat seemed less a pioneer, the first of its kind, than a survivor, the last of its kind - like the tunnel, a dead-end.

Not far from where the bat hung motionless, Fiona Mathews was busy moving boxes into her office in the University of Sussex's 1960s campus at Falmer. An enthusiastic, plain-speaking professor of environmental biology and chair of the Mammal Society, Mathews had just arrived from Exeter university and was determined to find out more about the greater mouse-eared bat. She had admired them on the continent, and had seen them landing on prey and covering it with outstretched wings. "We've caught some and you think, 'Blimey, that's big.' They come out [of the net] teeth first."

If there really is only one greater mouse-eared bat in Britain, with no possibility of reproduction, then it is as good as extinct. Seven other British bat species exist in such low numbers that no reliable population data exists. But technology such as bat detectors, which reveal bats by the sound of their echolocation, is helping better monitor populations. The Bat Conservation Trust's systematic monitoring of 10 species since the start of this century has revealed an unexpected picture: nine of these appear to be increasing in number. If true, it is yet another way in which bats have surprised us.

But counting bats accurately is difficult, said Mathews. They are usually counted where they are known to roost, but scientists have yet to work out a way of counting the number of roosts in an area. "Unless we know that, it makes it very, very difficult to understand what is going on with the population," she said. Current threats to bats seem to spring from misunderstanding of both human and bat nature. Today, every bat and every roosting site in the EU is protected by the EU Habitats Directive. But legal protection infuriates many home-owners and developers, and may encourage the furtive destruction of bat colonies.

Environmental legislation usually follows a "polluter pays" principle, but with bats, the person providing a home for bats is penalised, and must meet all the expense of surveying and providing alternative sites. The government is promising that after Brexit, public money for farmers will be based on the services they provide for the ecosystem (clean water, fertile soils etc). Mathews wondered whether a similar formula could be applied to homeowners who provide bat services.

"You can understand why people find it frustrating when they want to convert their barn and it's got bats in it and it's a complete palaver," she said. "Whoever has a bat roost is providing a service to the rest of the community, so there should be a community effort to make sure the bats are protected."

The second challenge for bats is another visible sign of society's supposed care for them: the bat bridges that span new roads. These trellises of wires hung between telegraph poles either side of the carriageway are designed to funnel bats up and safely over fast-moving traffic so they are not killed by cars and lorries when they follow their traditional foraging routes across new roads. Unfortunately, they don't work: bats are still killed by moving vehicles. And there is no funding to monitor how bats use these bridges, if at all, or to test whether there may be a design that does work.

"The idea that bats are going to cross a road in one place and not in lots of others is preposterous. They wouldn't have done that before the road was built. Why would they suddenly go to one crossing point? Yes, a bridge may be built on one key flightline [such as following a hedgerow] but the bats probably have 20 key flightlines," Mathews said. The evidence that bat bridges actually help bats cross new roads is poor, although there is stronger evidence showing bats willing to use tunnels under new roads and broader green bridges over them. Mathews was seeking to raise money to test different bridge designs before a road is built, and mystified as to why the Highways Agency pumped public money into unproven bridges. "They just want to deliver a project - something that ticks a box - rather than make stuff that works. That's a really bad use of public money."

Despite the roads, the regulations, the wind turbines and the barn conversions, Mathews feels there are grounds for optimism for Britain's rarest bat. The greater mouse-eared bat may have dipped in and out of extinction in Britain, but after decades of decline in northern Europe, the species is on the rise again in countries such as Austria. She believes it might be possible to find out more about the lonely bat's mysterious life. "My first question was: why don't we put a GPS tag on it?" she said. "It's already 16. It's now or never. We don't want to intervene and hasten the demise of this animal - it's that burden of responsibility - , but on the other hand, it does seem a rather wasted opportunity not to find out anything else about it. If it had been me, I would've been blitzing the place looking for evidence of greater mouse-eared bats, and I don't think anybody has." A new scientific review of British mammal populations states that it is "plausible" that other individuals are present, and could be revealed by exhaustive searches of potential summer roosting locations, or sites where they "swarm" in autumn.

Mathews will start doing just that this summer, putting out special nets - such as a harp trap, a large frame with strings between it which cause a bat to drop unharmed into a collection chamber below. "The same species on the continent is often found in churches and castles and big buildings. We could start looking at these sorts of places. We could also do DNA analysis of historic droppings. Perhaps it does go to France every summer and comes back? Surely it won't be the only one doing that? We could do some more work in the autumn, when these bats exhibit swarming behaviour. If there are others in the area that happen not to hibernate in the tunnel, it's possible they may turn up at that time of year."

Tagging, she admitted, won't be simple. At least the size of the greater mouse-eared makes it easier: you don't want a tag to weigh more than 5% of a bat's bodyweight, but the smallest GPS tags have now shrunk in size to just 1.5-2g, which makes it light enough to fix to the animal. But while tags are revealing hitherto-unknown facts about migratory birds from cuckoos to sandpipers, bat tags cannot be powered by lightweight solar because the wearer flies at night. When bats go underground, the tag needs a special programme to stop it constantly searching for a satellite and draining its battery. Mathews could use a combined GPS and VHS radio tag, but the latter requires a receiver, and if the bat disappears to France it will be out of range. The greater mouse-eared bat's life beyond its lonely tunnel will almost certainly remain unknown for a while longer.

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