But really, I knew what it was. Military training flights often pass over these Gwynedd hills. The roar was a jet fighter streaking right over my head. The disturbance was quickly over. In truth, there were few people to disturb.

I was walking in the Rhinogydd: often said to be the wildest and most remote mountains of Snowdonia (Eryri). The range is rectangular: moated to the north and south by the Dwyryd and Mawddach estuaries. To the west is a shoreline polka-dotted with static caravans, and to the east a nuclear power station. The Rhinogydd form a backdrop to Gwynedd’s holiday coastline – visible to anyone who has scaled the towers of Harlech Castle, or glanced up from their menu at Hotel Portmeirion. But few hikers walk them. The country is rugged, the footpaths scarce, faint or forgotten. You can queue for an hour to stand on the summit of Snowdon (Yr Wyddfa), but you can hike for days and see almost no one in the Rhinogydd.

The range has long seemed forbidding to travellers. In 1883, Jenkinson’s Practical Guide to North Wales characterised it as a “region of utter desolation”. And yet its rocky slopes have also acted as ramparts – guarding a number of prehistoric sites. There are Neolithic burial chambers and iron age hillforts, and the Rhinogydd are bookended by two bronze age stone circles: Cerrig Arthur in the south and the spectacular Bryn Cader Faner in the north. I plotted a two-day, 28-mile walk between the two along the backbone of the hills.

The name Rhinogydd derives from the Welsh word for “threshold”. At times – such as at dusk, when bats flit over old stones and the last bar of phone reception slips away – they feel like a threshold to the ancient past.

The first night I pitched at the Parc Isaf campsite and watched the sun set over the breaking waves of Cardigan Bay (there are cottages available for colder months). The next morning the needle of my compass guided me through the mist to more ancient sites. Sheep grazed the iron age hillfort at Dinas Rock. Wisps of wool blew about the burial chamber of Cors-y-Gedol, dating from Neolithic times.

“The western Rhinogydd was a busy ancient landscape,” said archaeologist Dr Toby Driver. “It may seem bleak, but it was alive. It’s probably more depopulated now than it’s ever been.”

I spoke to Toby on the phone: he told me his grandparents lived on the edge of the Rhinogydd and he has been visiting its ancient sites since he was seven. He said these fertile, west-facing slopes were deforested and laid into field systems in the Neolithic and bronze ages. Stone structures – such as Cors-y-Gedol – were often places for burial or cremation. They were possibly also places from which revered ancestors could watch over their descendants.

“These are the first pieces of architecture people ever built, when they started farming and stopped hunter-gathering,” Toby said.

Today, there are several working farms in the Rhinogydd, though some have been lost. I saw a number of buildings turned into holiday lets on my walk. Some predict that hill farming will become uneconomical in future generations: a 6,000-year-old agricultural practice will end, forests will regrow and a circle will be complete. But for farmers in Eryri, such “rewilding” is a byword for expulsion. These ancient sites are marks of ownership – stones that guard the land, and also the bones and ashes of those first ancestral farmers.

Not all tombs in these mountains are ancient. North of Nantcol, the landscape closes in: moorland turns to a maze of boulder and bog. I waded through a sea of bracken, tracing paths invisible to the eye – but that could be sensed with a probing shin. On the so-called Roman Steps – along which ghostly centurions are said to tread – I heard a clatter of pebbles, and watched a herd of feral mountain goats trot past. Later, I heard a clink of metal under my boots and knew I’d arrived at another historic site.

On 6 February 1945, Lancaster NE132 departed RAF North Luffenham, on a training mission bound for Cardigan Bay. There were seven men on board: the forecast warned of storms. That night, people in Harlech saw a red tinge to the clouds over the mountains. The debris from the flight still lies on the heights of Rhinog Fawr today – a mess of ripped fuselage, rivets and rust. It is one of dozens of plane wrecks found across the summits of Eryri, strewn like shipwrecks on a shore.

Being hard to find, Lancaster NE132 is one of the more extensive wrecks. I sat for a while wondering what would be left of the plane after another 80 years of Welsh weather. Of the seven men who perished, the bodies of two were never found in the wilderness.

On the last leg I passed the peak of Moel Ysgyfarnogod, and a view opened out. Distant plumes of steam rose from the engines of the Ffestiniog Railway. There was the pyramid of Snowdon, and the Llŷn peninsula tapering out to sea. I followed a path up to Bryn Cader Faner, set on a pulpit of rock overlooking this scene. This magnificent stone circle dates back more than 4,000 years, its stones leaning outwards, making it look crown-like. As with all stone circles, its meaning and function are lost in the mists of time. To those who built it, the circle may have represented the sun, the turn of the year, the cycle of life. Its setting high in the Rhinogydd is typical of many circles: it may have derived some power from its proximity to the sky.

Occasionally flowers and messages are left at the stones, deposited by pilgrims who climb up here. My new book, On This Holy Island, examines how megaliths retain a power for some in the present day: the stones have no written creed and ask nothing of you; they let you make your own meaning. Against the everlasting rock, modern anxieties seem ephemeral. Hot heads cool when pressed against old stones.

The mist thickened as I turned to leave Bryn Cader Faner. I had read that, in the 1920s, a curious farmer had wanted to excavate the middle of the circle – but every time he tried, a roll of thunder warned him off. A great boom echoed in the crags as I departed the Rhinogydd. It was the RAF again, or so I’d imagine.

On This Holy Island by Oliver Smith is out now (Bloomsbury). To buy a copy for £18, go to guardianbookshop.com