South of it, flanked by state offices, a broad boulevard leads to the city's university and a quiet park of paths and pines. There, among the trees, stand the familiar white ranks of a small British military cemetery. Each headstone marks a young man's life lost in the Second World War. Seven are carved with the names of secret agents of Britain's Special Operations Executive.

Those seven hold some meaning for me. A fellow agent, who survived, was my grandfather, Captain Ian Merrett, who parachuted into occupied Albania in 1943 and spent ten months in the mountains. I never knew him. He died young and remains a distant figure. But in the last few years I have dug pretty deeply into what SOE's agents had gone out there to do, and what has come to light very powerfully are the terrible ordeals he and the others had to face and the awful risks they ran. Hidden for decades in diaries and classified files and the memories of survivors, their story is a grim one, extremely so at times. It is also remarkable.

SOE's job was to encourage subversion and carry out sabotage behind enemy lines: in Churchill's famous phrase, to "set Europe ablaze". Early on, its principal commitments were in northern Europe; but in 1943 it found itself tasked, too, with intensifying the resistance across the Balkans, which had fallen under Axis influence early in the war. Soon, dozens of small missions of specially-trained troops, almost all of them British, were being dispatched to find and encourage resisters, blow up bridges, ambush convoys and call in airdrops of arms and ammunition. That, at least, was the plan.

Missions bound for Albania had little concept of what was waiting for them. It was Axis-occupied; they knew that. Mussolini, Italy's fascist dictator, had invaded in 1939. His men stayed for more than four years, and when Italy surrendered the Germans took over. But not one SOE officer had prior experience of the place and the only expert available to brief them beforehand was a mildly eccentric folklorist, Margaret Hasluck.

A farmer's daughter from Drumblade, near Elgin, and the widow of an eminent archaeologist, Hasluck had lived in Albania for 20 years before the war and was an authority on the phenomenon of the Albanian blood feud. At SOE headquarters in Cairo she tried to teach her pupils the language by having them learn Albanian nursery rhymes. For one bemused young officer, "it was a bit like having Enid Blyton in charge".

The guerrilla life into which he and the rest were then catapulted was one of appalling privation and danger, of squalid villages, burning homes and civil war. The poverty encountered was extreme. The first team to parachute in was led by a thrusting 24-year-old Scot and future MP for Inverness, Neil "Billy" McLean, a direct descendant of "Gillean of the Battle Axe", 13th-century forebear of the clan Maclean. Before long, McLean was recording in his diary how peasants in the mountains were digging up dead Italians for clothes.

McLean, an Old Etonian, was a regular officer in the Royal Scots Greys, who had fought a guerrilla war once already, in Abyssinia. Yet the backgrounds of the young men who volunteered for this hazardous work were diverse. One, whose daring and violent attack on a chrome mine was perhaps the most significant act of SOE sabotage carried out in Albania, had spent eight years as a Royal Air Force nursing orderly. My grandfather bluffed his way through his SOE application with tales of a Cambridge education. A train-driver's son from Brixton, he had never been near the place.

Another officer sent in to Albania was the actor Anthony Quayle. Forced for months to hide in scorpion-filled caves in cliffs high above the Adriatic, he had a particularly unpleasant time. Once, as he tried to paddle a small party out to a waiting ship for evacuation, his rowing boat overturned in the surf and three men with him drowned.

Colleagues thought highly of Quayle. "I feel he likes me, as I like him," one wrote privately at the time. "He is an actor and seems to want to do only one thing – get the war over with."

"Big, immensely reassuring, very amusing, patient, kind," another remembered – "in every sense a very good man."

One volunteer was a 24-year-old army doctor, 12 months out of St Thomas's medical school. His job was to do what he could, with the pathetic resources he had, to patch up wounded guerrillas. Within days he was pulling bullets out of wounds and sawing off limbs before his mountain hospital was overrun by the Germans, who then slaughtered all his patients.

"Doctors are few and folklore handed down from father to son is the chief guide to medical treatment," he lamented later of the conditions in which he had to work.

Lice, disease and the constant threat of capture and death plagued McLean and the men who followed him. And winter, when missions were chased high into the snowbound peaks, was horrific.

"At dusk the road is safely re-crossed and a forced march made up the mountain," reads the diary of one hunted officer. "This is as steep as the side of a house, very rocky and slippery and in our weakened state a terrible trial … The effort required to maintain and recover one's balance is truly appalling – none of us has ever experienced so severe a trial of physical and moral strength and endurance.

"At 2100 hrs, having nearly reached the summit, the guides, after much questioning, have to admit that they have lost the way! The decision is taken to make camp but if we are to survive the night fires must be lit. Our clothes are already standing out stiffly round us like boards and every twig and branch is heavily covered in frost. To stand still for a moment is to court frostbite and death."

The dangers took their toll. Of the first 50 men sent in, one in three died or was captured. The dead included the officer who wrote that diary entry: 33-year-old Arthur Nicholls of the Coldstream Guards.

A Cambridge-educated stockbroker with family hailing from Aberdeen, Nicholls had volunteered for a Balkan mission from the safety of an SOE desk job in London. He had hardly parachuted in to Albania before it all began to go wrong. With his team ambushed and scattered, he was forced on the run, with no medical supplies and little food, through mountains covered by 4ft of snow. Badly frost-bitten, he remained on the move in an astonishing effort to locate another mission and when finally found was starved, gangrenous and had dislocated a shoulder in a fall. Nicholls insisted on carrying on his work but septicaemia had taken hold and he died a few days later.

"He set an example of heroism, fortitude, courage, leadership, the will to win, and devotion to duty which has seldom been equalled and never surpassed," reported the SOE officer who found him. "He carried on far longer than could normally be considered humanly possible, and this undoubtedly caused his death." Nicholls was posthumously awarded the George Cross.

Today in the Albanian mountains it is hard not to gain a sense of what wartime conditions may have been like; and traces of the British can still be found. Sixty years on, there is more wealth about, though not a lot. Satellite dishes stick to the slates of some of the most isolated stone cottages; 4x4s can be found in areas no earlier vehicle could penetrate. Yet the formidable peaks are unchanged, while countless villages beneath them eke out an existence at a subsistence level that has changed little in generations.

Look closely enough, and the evidence of the British takes several subtle forms. Close to old SOE dropping grounds and betrayed by redundant handles, rusting parachute-containers patch chicken-coop roofs and pigsty walls. The original contents of more than a few may also be up there, somewhere. In Tirana, not long after the Kosovo war, I met a man running a United Nations program aimed at encouraging mountain villages to exchange their personal weapons for UN aid. It took a while, he told me, before his team understood why so many British Sten guns and Bren guns were being handed in. Most, he added, were still in working order.

As well as relics, there are memories. In villages close to the coast, women who were children at the time recall Quayle and his men as huge figures who handed out chocolate and stomped around in enormous boots.

Elsewhere, elderly partisans speak of nights spent covering British soldiers sent to blow up bridges, of dropping down from the mountains and hiding in the dark as the charges were laid and fuses lit. More than one remembered his superiors telling him: "Do not speak to the British; but die for them if you have to."

But the memories are not always there. In many of the most remote villages, something becomes quickly and horribly apparent: the ruthlessness with which Albania's communist leaders dismantled the old tribal strongholds and structures in the aftermath of the war. This had been done on a vast scale, the aim being to crush and prevent any shred of anticommunist opposition. Hundreds were arrested and imprisoned, interned or worse.

Albanians who had worked with the British became particular targets. The communists, who themselves had risen to power on the back of the British-armed partisan movement, saw SOE attempts to arm rival bands as efforts to prop up the hated old order: King Zog, chiefs and the rest. Official memories of British help for the partisans were short.

There is no better illustration of this twist than the story behind the British cemetery in Tirana. Today's headstones were erected just 15 years ago, after communism collapsed and outsiders were let in. They also stand only in the approximate area of where the graves, laid out carefully at the end of the war, are thought to be. Within five years of the British leaving, the communists had dug up and destroyed all trace of the original cemetery.

Readers can buy Roderick Bailey's The Wildest Province: SOE in the Land of the Eagle published by Jonathan Cape, priced £25 for the special price of £22.50 including free UK p&p. To order, tel: 01206 255 800 and quote the ref The Scotsman.