The Sun is rising on a calm and cloudy morning in late February 2017, and Jamie Sneddon and I have an important collection to make. After a short drive along the north-east coast of Scotland – passing open fields, detached bungalows, and blooming bushes of gorse that shine with a radiant yellow under the grey sky – we arrive at the muddy entrance of a farmyard.

Many of the locals here in the remote Scottish Highlands are crofters: they nurture and trade certain root vegetables and small numbers of livestock and poultry, a lifestyle first developed in the 19th Century. After opening a red and rusting gate, we disturb a vocal gaggle of geese and a few chickens. Through the wire fences that border the farm, we can also see a small flock of sheep.

However, Sneddon has only one animal on his mind: a cat. He is hoping to catch a stray tomcat that rules the yard. The previous day, he had baited a small cage inside one of the farm's stone outbuildings with mackerel – cheap, smelly, and easy to split into portions – and cat food.

It worked. After noticing the trap door had shut during the night, the landowner placed a 12-pack of ale on the metal cage, both as a gift for Sneddon and as a weight for added security. Peering into the cage in the morning, we can see that this was a wise precaution. The black-and-white tomcat is huge, thick at the shoulders with muscle, and he has the classic widened face that only develops in sexually-mature males. His nose is covered in claw marks. This is his turf – his farm, his females – and he has been fighting for it.

Luckily for Sneddon, the cat seems tired out and remains somewhat somnolent as he carries the cage to the boot of the car. I carry the box of beers, a much lighter cargo than the big tom.

But the cat is the true gift. Over the next few hours, he transforms from an aggressive stray into a treasured tool of conservation. Ultimately, it could help to protect one of the rarest creatures on Earth: the Scottish wildcat.

These cats could number as few as 35 individuals, fewer even than the widely-cited "world's rarest cat", the Amur leopard. Sneddon is project officer with the non-governmental organisation Wildcat Haven, which is working to save them.

In the hills, fields, and gullies surrounding the farm, the isolated populations of Scottish wildcats are within walking distance. The life of this tomcat is the story of their future survival.

Scottish wildcats are formally known as Felis silvestris grampia. They are a subspecies of the larger wildcat group that prowl through much of the Old World. To Scottish people, they are Highland tigers. Although they are about the same size as domestic cats, they can be twice as heavy.

Wildcats came to Britain via Doggerland, a huge expanse of marshes and tundra that connected Britain to the European mainland during the height of the last ice age around 12,000 years ago. It is sometimes called a "land bridge", but that is misleading since it was the size of a country.

Nobody knows when wildcats first moved to Britain. But they became permanent residents around 6,500 years ago when the Earth warmed, the ice melted and the North Sea swept back over Doggerland.

Britain was an island once more, and the wildcats that had crossed Doggerland were cut off from their relatives in Europe. Over generations, they evolved thick grey stripes that run down their flanks and encircle their broad tail, camouflaging their presence in Scottish pine forests.

The wildcats have been shot and trapped for centuries in Wales, England, and southern Scotland. But in the Highlands they were revered as icons.

At once fluffy and fearless, they are exceptionally vicious when cornered. Their wild nature was celebrated by many Celtic groups. For instance, the sigil of Clan Macpherson is a snarling Scottish wildcat, and their motto, "Touch not the cat [without] the glove," is both a warning and a recommendation.

For the wildcats, northern Scotland, where the original stands of Scots pine are still rooted in the mountainsides, was a refuge from human persecution. This protection was reinforced by a 1988 amendment to the 1981 Wildlife and Countryside Act, which made it illegal to shoot or even disturb a wildcat. That was a huge step for the wildcats, which had been slowly increasing in number since 1914, when only a couple of relict populations were left.

Around the same time, however, researchers were realising that they had a lot more work to do. It had become apparent that the biggest threat to wildcats was not humans, but their pets.

Pet cats are more numerous than any other cat species. They were introduced to Britain by the Normans in the 11th Century, and perhaps by the Romans much earlier. In Scotland, there are nearly 200,000 stray domestic cats. They often stay close to human habitations: feral cats that are completely independent of humans are rare at these northerly, bitter latitudes.

For hundreds of years, wildcats have been breeding with domestic cats (Felis catus). The proof is printed in the wildcats' fur, which is not as stripy as it once was: dots and splotches of grey have replaced neat lines. Over the centuries, wildcats have become ever more similar to tabby housecats, and less like miniature tigers.

Slowly, with each hybrid litter, Scottish wildcats are being domesticated, diluted into a form that strains the definition of "wild". Instead of hunting alone in the wilderness, they often hunt from garden bird feeders, devastating the local populations of rare birds.

It is possible that this hybridisation started 2,000 years ago. For that reason, some researchers believe that no wildcat is truly wild anymore. All are hybridised – domesticated – to a degree. This idea has been supported by genetic tests that found domestic DNA in old wildcat specimens.

But there are still a few wildcats that are boldly striped, that eschew all contact with people, and that hunt hares, rabbits, and other small mammals over large tracts of the Scottish highlands.

These are the cats that Sneddon and his colleagues hope to save. To do so, they leave them alone. They touch not the cat.

The Wildcat Haven team has a motto of their own: "Keeping wildcats in the wild where they belong." As Sneddon and I drive around the meandering roads near Wick and Thurso in north-east Scotland, this is written on our car's front doors, underneath a logo of a wildcat formed entirely from black and grey stripes. Seeing this image as we drive past might be the closest many people will get to a true wildcat.

After collecting the big tomcat, Sneddon and I visit many other landowners, all of whom feed stray cats in return for keeping the mouse and rat populations in their barns down. Such "mousing" is a symbiotic relationship, but it can also be harmful for the cats. Living in human barns and outbuildings also means living with roads and cars; I see plenty of dead cats in the roadside mud. What's more, inside the buildings domestic cats can live in large colonies numbering over 50 individuals, which become breeding grounds for disease.

With the landowners' permission, the team of veterinarians and volunteers that make up Wildcat Haven spend the four weeks of February trapping and neutering strays, all the time accompanied by a representative from Humane Society International. If the cats pass all health checks, they are returned to the same area from which they were caught.

"It's a paradoxical project," Ewan Brennan, volunteer field biologist for Wildcat Haven, says later. "To save wildcats, we work almost exclusively with domestics."

After the morning farm rounds, we drive the black-and-white tomcat to a nearby rented veterinary clinic. The first step is a quick injection with an anaesthetic mixed with painkillers. He does not seem to notice anything at all, his green eyes unblinking. "Strays don't flinch," says Nick Morphet, the senior field vet for Wildcat Haven and the man holding the needle. "They've had a hard life."

In five minutes, the big tom is fast asleep and can be carried safely to the operating table. It is not an easy task: he weighs about 5.5kg, nearly as big as domestic cats get. "Oh yeah, he's a bruiser isn't he," says the veterinary nurse, rubbing his flanks for any sign of injury. She feels something that might indicate a damaged organ, but Morphet thinks it is just a lumpy rib. And straightaway, Lumpy Rib joins the other notable stray names, including Scrapyard Cat, Alley Cat and the enigmatic Fluffy.

Lumpy Rib is placed on his front with his legs splayed outwards. I touch the jowls that surround his face. Under the soft white fur, the skin is tough and leathery, and would shield his neck from a rival's unsheathed, horn-coloured claws. Morphet tells me the thick skin can blunt his needles.

After finding no evidence for a microchip, which would identify Lumpy Rib as someone's beloved pet, Morphet takes some blood samples that will be tested for diseases. Calicivirus (a flu-like ailment) and conjunctivitis can be suggestive of poor living conditions, but the feline immunodeficiency virus (FIV) and feline leukaemia virus (FeLV) are of more immediate concern. Not only are they fatal and without cure, they are also highly infectious, so could spread from stray cats to wildcats.

In 2015, this threat came close to a reality, when researchers from the University of Edinburgh discovered evidence of FIV in two wildcat-domestic hybrids found dead in the western highlands. Such hybrids act as vectors of genes and diseases between wild and stray populations, so it is vital to make sure no infected cat is returned to the environment.

It does not take long to determine Lumpy Rib's fate. Morphet decants a small drop of the cat's blood onto something that looks like a white doorbell, but which tests for FIV and FeLV with near-perfect accuracy, then starts the stopwatch on his smartphone. We have to wait ten minutes for the test result.

The well-lit operating room is not filled with confidence. The big tom's docile demeanour and the claw marks on his nose – the principal way viruses spread from male to male – suggest he might be FIV- or FeLV-positive. If he is indeed a carrier, the team would put him down with a humane injection. Even if he did not pose a threat to the wildcats, life with either virus would soon become unbearable.

After the ten-minute mark passes, we all breathe a sigh of relief. Lumpy Rib is healthy. This makes Sneddon and me almost cheer with delight: partly because putting down any animal is unpleasant, but also because big males like this are crucial to the conservation of wildcats.

"He's our bouncer," says Sneddon. Lumpy Rib will hopefully prevent any females – both stray and wild – from having kittens. His presence should also reduce the chance that another male will move into the area, start breeding, and spread disease. If the team were to kill stray cats like Lumpy Rib, others would simply move in and take their place, an unhelpful phenomenon known as the "vacuum effect".

Instead, the team takes a bit more time and effort, and neuters the strays before re-releasing them.

This "trap-neuter-return" protocol requires a lot of planning and patience, even though the surgery itself only takes a few minutes for males and around half an hour for females, whose ovaries are not easily accessible. Used across the globe since the 1960s, it is a tried-and-tested method to control feral cat populations.

In 2014, the Wildcat Haven team succeeded in ridding the 250-square-mile (650 sq km) Scottish peninsula of Ardnamurchan of all of its fertile and infectious strays. A few may still remain, but the chances of a wildcat breeding with another wildcat here is greatly increased.

The 2017 project has the same ultimate goal, but the scale is unprecedented.

A trio of deep lakes – Loch Ness, Loch Oich and Loch Lochy – splits the Scottish mainland in two, separating 7,000 sq miles (18,100 sq km) of northern highland wilderness from the dense cities and farmlands of the south. This diagonal line of water lies along an ancient rift valley called the Great Glen. There are only three small land bridges across it. One of them borders Inverness, the "capital of the highlands".

To O'Donoghue, the Great Glen is a natural boundary for a wildcat haven spanning north-west Scotland. With every stray that is neutered above this line, the Scottish wildcat's future becomes that little bit more secure. But clearing all of north-west Scotland is a huge task for such a small team, and funding is tight: the volunteers, including Sneddon, work long days with little sleep and only have their expenses paid.

However, they are not completely alone in the wilderness. In 2017, Scottish Wildcat Action (SWA), which is partly funded by the Scottish government and backed by 20 conservation groups and the IUCN, also began trapping and neutering stray cats in Morvern, a jagged peninsula just a few miles from Ardnamurchan.

O'Donoghue and the rest of the Wildcat Haven team welcome such efforts in the field. But at the same time, they are actively campaigning against another of SWA's priorities.

"The government action plan has a heavy focus on captive breeding, and there is a license in place to capture wildcats," O'Donoghue says. "We are diametrically opposed to that. We believe that the Scottish wildcat should, and can be, conserved in the wild."

The trouble is that so little is known about the overall state of the wildcat population, says David Barclay, the project leader of SWA's captive breeding programme at the Highland Wildlife Park. He says SWA's approach is a necessary contingency plan, a safety net for the wildcats.

"If there are no viable populations, then by that definition it doesn't matter how much conservation work is done in the field," says Barclay. "Even if you remove all the threats, if there is no population strong enough to build itself back up, [the Scottish wildcat] will go extinct."

In 2013, the SWA designated six "priority areas" – Angus Glens, Strathbogie, Strathpeffer, Strathavon and Northern Strathspey – where Scottish wildcat populations seem to be healthy, based on auspicious camera trap surveys, local sightings and 43 faecal samples. For now, no cats are to be taken from these areas, but Barclay says that his team plans to capture males and collect their semen. This can be used for artificial insemination in the captive population, making its gene pool more diverse.

"Outside a priority area, where a wildcat is at high threat from localised extinction, or persecution, or further hybridisation, that's an individual that we want to bring into captivity," says Barclay. If it passes a string of tests to prove it is not a highly domesticated hybrid, or simply unhealthy, "that cat would go into the big off-site breeding enclosure".

At the moment, this enclosure is empty, and O'Donoghue hopes it will remain that way. While Barclay sees its mesh fence as a safety net, O'Donoghue sees it as a false sense of security. Even if breeding is successful, a 1996 review by the IUCN Cat Specialist Group reported a mortality rate of 70-80% for wildcats reintroduced from captivity in mainland Europe. In 2001, an updated review concluded that that out of four reintroduction projects in Europe, two were failures, one was inconclusive, and one was a success.

There are other concerns. Since its inception in 2013, the SWA's methods have come under scrutiny from conservationists and animal welfare organisations.

In April 2016, Ecologist reported that Wildcat Haven had obtained SWA's trapping license under freedom-of-information laws. The license states that, if a stray cat is captured and is not deemed suitable for captive breeding, the landowner can kill it with a shotgun blast to the head. In response, the charity Cats Protection started a petition against the project.

"We as an organisation don't shoot cats," says Barclay. "But we want to ensure that the way landowners dispatch a cat in a cage trap, which would be shooting, is the most humane and quickest way possible."

Regardless of whether shooting is indeed the most humane method of killing these cats, removing them will probably mean that more cats move into the territorial vacuum left behind. Furthermore, if stray cats are seen as disposable creatures rather than precious tools of conservation, people might stop supporting the more effective catch-neuter-return projects. "It will impact the Scottish wildcat, which is the last thing we want," says O'Donoghue.

At the Highland Wildlife Park, where the SWA's breeding enclosure has been built, concerns still abound. In late 2016, the Times reported that 21 Scottish wildcats were born between 2009 and 2012, but five had died for unknown reasons. And strangely, 14 had been neutered, including two – called Brave and Merida – that were previously deemed invaluable to the conservation of wildcats. In other words, the captive breeding programme had taken steps to prevent breeding.

Barclay says SWA was trying to avoid a population boom in captivity, which would have resulted in "many, many animals with no homes to go to". However, O'Donoghue says that a population boom is exactly what the critically-endangered wildcats need, and that most zoos would bend over backwards for wildcat kittens. "Every single individual counts," he says.

At four o'clock in the afternoon, Sneddon and I are invited for a cup of tea by a local woman. She wants to see some camera-trap footage of healthy adult wildcats, stalking through their patchwork of grass, juniper, and gorse. Her face lights up as Sneddon points out the distinctive bushy tail and thick stripes of a wildcat that lives in the neighbouring glen, half an hour's drive away.

In some areas where the team has been working, kittens have been reported. Their births do not prove that the populations are viable, but they are a promising sign.

After we finish our tea and nearly a whole packet of chocolate fingers, the three of us go for a walk under a blanket of amber clouds that soak up the last rays of the sun. After about 10 minutes of walking through reed beds and thick mud, we find some cat faeces. It lacks the spiralled end of fox poo, so the question is whether this scat was from a stray, a hybrid or a wildcat.

Behind the poo is a small island of crumbling dry stone wall, a perfect spot for a cat to scent-mark among the waving reeds. To identify the territory’s owner, Sneddon sticks a piece of wood firmly into the soft ground and attaches a camouflaged camera trap, its lens pointing at an area of the wall that has fallen near to the ground, providing a gateway through the stone.

Our host bends down to help him tighten the straps. "I've been waiting for 18 months for this," she tells me. "People think I'm crazy, but we have wildcats here in Caithness. It means the 'Land of the Cats'." Her eyes might be watery because of the cold air that sweeps through the glen, but I suspect otherwise.

"Poo is conservation gold," Sneddon says later. Without it, he would not know where to place his camera traps and would be (almost literally) shooting in the dark.

Later, as we drive back to the big tom's farm in the pitch black, Sneddon meditates on the camera-trap site we just left.

"That wildcat up there with no clue, completely oblivious that it's part of an endangered species, might die there," he says. "But I'd prefer that than for it to live its last days in a cage."

In the farmyard once more, Sneddon says I should release Lumpy Rib from the trap. He may have been neutered, but he is still very heavy and I struggle with the cargo as he sits inside patiently, characteristically unperturbed. With a little encouragement from gravity, he returns to his home, skipping heavily over the muddy puddles. His black-and-white fur blends into the night.

This story is a part of BBC Britain – a series focused on exploring this extraordinary island, one story at a time. Readers outside of the UK can see every BBC Britain story by heading to the Britain homepage; you also can see our latest stories by following us on Facebook and Twitter.