Sometime around 1680, the steward of St Kilda, a man called MacLeod, his wife and a "good crew" were sailing from that island home to Harris, when a great storm blew up. It drove them northwards for hours, north even of the Butt of Lewis, until at last it cast them ashore on the island of Rona. They managed to save themselves and their provisions, but their boat was destroyed.

In the drama of their scrambling up the rocks - there are no beaches - no one came to help. Perhaps it was night, or perhaps they'd landed unseen on the island's north side. But it must have seemed strange, as they filed through fields towards a village, that they could smell no smoke. Rona was inhabited; it could support about 30 people and had done for centuries. There was a chapel, already ancient, and an oratory built by St Ronan himself, and a huddle of thatch-roofed houses dug into the ground. MacLeod's party must have called out a Gaelic greeting, louder and louder, but no one replied.

Later MacLeod recounted how they had buried the bodies they found. There had been a calamity - a plague of rats had come ashore, "but none knows how", and devoured the people's crop. No supply boat had reached the island that year. "So those deceased persons ... died of want."

More people have heard of, indeed visit, St Kilda, with its extravagant cliffs and its own affecting narratives of isolation and abandonment, but Rona is even further out in the Atlantic: 45 miles north of Lewis, on the same latitude as Orkney. The maps give every crag and inlet their Gaelic names, but no one is there to speak them now. There were attempts at resettlement. Tenant farmers carried on for another 150 years, but in 1844 the last family quit and went back to Lewis. With that, the island was finally abandoned.

There is little to it; a mile and a half long, it has one 300ft hill, Toa Rona, which descends westwards to become a ridge, which in turn slopes down to the sea in rocky promontories. A flat peninsula runs out on the northern, wilder side. On the south-facing hill, though, the land is almost lush. There the ruined chapel remains, as does the forsaken village and the long-overgrown farmland. Rona's roll-call nowadays is limited to yachtsmen, lighthouse engineers and shepherds from Lewis who arrive perhaps once a year to round up the half-wild sheep. And naturalists: there is a tradition of parties of naturalists heading for Rona, for the seals and birds. Kittiwakes and guillemots breed on the cliffs; there are great black-backed gulls on every knoll. Aside from the lighthouse - a modern one, built to warn oil tankers - there is just one usable building: a bothy that houses some field biologists who come every autumn to study the island's grey seals. And there is the sea, and the sound of the sea, everywhere and always around.

Our own island-going had been arranged by a man called Stuart Murray, who is well known among Scottish ornithologists. Murray was for several seasons warden at St Kilda; he has conducted important surveys of sea-bird populations, including one on Rona. To their aficionados, the far-flung Scottish islands sing siren songs of vast skies and salt-winds and sea-birds. They speak of occupation and relinquishment and an austere spirituality. But how to get there? Murray's ploy was simple. He chartered a motor yacht called the Poplar Voyager (he knows the skipper, Bob Theakston, from previous ventures), then set about offering places to 11 other people of his choosing: naturalists, ecologists, photographers, an archaeologist, an authority on early Christian monuments - all with our interests and obsessions and experiences. It is the kind of call you dream of, sitting at your desk in January, or stuck on a bypass. Wonderful to know it will come again, sunlight and surf, pink thrift and gulls' call.

We sailed from Kinlochbervie on the mainland. The skipper warned it would be a bit rough, and when he put out of harbour and turned north-west, the sea was lumpy on the horizon. Six hours across dark blue sea, with waves breaking to white. When free of blowsy clouds, the sun was intense; it picked out the occasional gannet as a white dart. But the wind was freezing. To be out on deck as the boat rose and fell meant being wrapped in waterproofs, hats, gloves. Bonxies - great skuas - patrolled overhead, and parties of guillemots or puffins went whirring by just above the water. After an hour, with the cliffs of Cape Wrath fading behind, there was a moment of shouts and excitement: three killer whales had appeared, females, their black dorsal fins cutting quickly through the water, a swift vision of black and white just beneath the surface. Another hour, and only a few die-hards remained standing. By then I was lying flat on the rear deck, with one of my shipmates curled clinging to the rail, another leaning like a corpse against a chair. When, in mid-afternoon, the shout came that you could at last see Rona, my first sight of this far-flung jewel was while retching over the side.

A couple of dozen grey seals, hauled out on low rocks, lifted their whiskered faces to watch as Bob slowed the engines and manoeuvred the Poplar Voyager carefully past them into a steep-sided inlet. The seals were sanguine enough, but guillemots stacked on the cliff-ledges above greeted us with gargled screams.

The idea that remote islands are somehow "timeless" is a nonsense. Of course you want to slow down and fill your mind with space and sea, to examine every inlet and flower, but unless you want to be marooned, you always have to bargain with the weather. There are no safe anchorages on Rona, and Bob was concerned about the east wind. If it rose a couple of notches, as was forecast, we'd have to turn and leave again, simple as that. But we'd have the night at least, and probably the next morning, too. We went ashore in the tender, each choosing our moment to jump as it leapt in the swell, then clambered up slippery rocks on to the hillside. Just that small elevation, a hundred feet or so, gave an astonishing view: a green morsel of an island, already dipping back towards the sea, and the sea shifting away forever.

The seal researchers' bothy stands proud on the island's south side, like a garden shed pretending to be a lighthouse. A vague path led uphill towards it. A bonxie flew alarmingly close overhead, big and brown, but it didn't attack. Always there was the sound of surf, beating on the rocks.

There was a plan: after we'd pitched tents and had explored a while, we'd eat aboard the boat, then just as it was getting dark, we'd assemble in the derelict village. The day was long: it was almost 11 before the light drained from the sky. The village is encircled by fields that are still clearly defined on the ground. They're not square fields, but the old so-called "lazy-beds" - long, heaped-up mounds which alternate with drainage ditches. They rise and fall in waves, as though the land, being so close to the ocean, had assumed the same sea-swell. A narrow path winds through the lazy-beds to the abandoned village houses. Only when you're among the walls do you realise that's what they are: rough stone walls of dwellings, built half into the ground.

As night fell, the breeze grew colder. Darkness pooled in the ditches and the roofless shells of houses. Though the sky was clouded, a pewtery light lingered on the sea. We were gathered in the ruins for a purpose: one of our party, John Love, had established himself in the lee of a wall and set out a few tools: minuscule pliers, a small ruler and a spring balance. As night came on, quietly we listened to the surf and to the seals crooning mournfully from their rocks. Far over the sea, a full moon was rising, brightening the bank of cloud that was waiting to receive it. A solemnity fell over everyone, as we waited for things to begin.

Then, when it was quite dark, someone started chortling. Not a person, but a pixie. John and the other birders smiled and roused themselves. Again, and more: from gaps in the old walls came wonderful sounds of pixies and elves, burbling, chattering and riding little two-stroke scooters. The village walls, which we in our dull anthropocentric way call "poignant" and "silent", were alive with gleeful, tin-toy, chatterbox sounds; and then something flew quick and bat-like through the dark.

This is one reason ornithologists come to Rona. Leach's petrels are rare birds that live out at sea, and which come ashore only to breed. They nest in burrows, usually on clifftops, and come and go by night. To catch and ring them requires a special licence, which Love holds. He had spent the early evening erecting two mist-nets (a bit like badminton nets) across gaps between walls. Now the birds were plopping in like shuttlecocks.

It does them no harm. They didn't flutter, they just waited for deft hands to disentangle them. After it had been taken from the net, each bird was put in a cotton shoe-bag, and the bag carried to Love. We who'd never seen petrels before crowded for a look as he removed the first one. About the size of a thrush, but smoky dark, they have a tube nose like a fulmar's, and exquisite, tiny, black webbed feet. (The name petrel comes from Peter, who walked on water.) Love showed us the forked tail - the bird's full name is Leach's fork-tailed petrel - and demonstrated how best to hold the bird so it feels secure; you enfold it in your hand so its head sticks out between your middle and index finger. The fine feathers on the petrels' heads reminded me of the inside of puffballs: a rich, musty, dusty brown, but with a quick dark eye.

Love measured the length of each bird's wing, then he took a minuscule ring and, with the pliers, closed the ring around the bird's leg. Each ring is numbered, and for a while my small task was to act as scribe, noting by torchlight the number of the ring as he read it out, and the weight and size of the bird to which it was being attached. Before the birds were released they were weighed. Then, if you catch an individual again in the future, you'll know how old it might be, how well it's faring, if there are fewer or more than there were 10, 20, 50 years ago. Many of the night's birds were "re-traps". Though small, they can live for more than 30 years. How to weigh a petrel? You slip it back into its cotton bag, then hang the bag from your spring balance, being mindful to deduct the two grams the bag weighs: 48, 47, 50 grams, a scant two ounces of feather and bone - yet petrels winter far out at sea, weathering the storms. Then they're released, with a casual throwaway gesture that gets them airborne and away, none the worse.

By about 1am, after the chill hours lying queasily on the boat's deck, I was bitterly cold, and though the petrel party would go on till dawn, I was ready to retreat to my tent. Perhaps it was the effect of the cloud-obscured moon, but the island was gilded in a strange bronze light. It had been my birthday, and I'd been heaped with gifts: sea, and orcas, Leach's petrels and seals singing their loopy, consoling songs. As I climbed, fully clothed, into my sleeping bag, I noticed that my hands smelled. It was a funky smell, almost sexual, dusty and oily at once, the smell of petrels, like a mushroom made of whale breath and herring-scale.

Were it not for that lingering smell, I might have thought the petrel business a dream. The morning sunshine was bright, and full of sea light. There, again, was the vastness of the sea. The wind was holding off, but clouds were building. We had breakfast on the boat, then went ashore again. I made my way across the hill and through the lazy-beds to the village and St Ronan's chapel, so to see them by daylight. The nets, of course, were gone. Love and the others had stayed till about 4am, and caught about 100 birds. Now the low walls, with their coats of turf and lichen and tufts of sheep's wool, were again inscrutable.

The doorway to the chapel is so low you must creep through bent double. Within is a small rectangular nave. There is no roof now, only the dry-stone walls remain, but even with the sky above there is a feeling of age and sanctity. Great age: it's 1,200 years since St Ronan arrived in his boat. Leaning against the walls are some broken quernstones and a number of rough stone crosses, stained with bird droppings. Twin symbols of Rona life, you can sense toil in the quernstones, a residual paganism in the crosses.

In the chapel's eastern wall, a further low doorway opens into the tall, corbelled chamber of the saint's oratory. The lintel is hewn from quartz; the whole structure feels Neolithic. Inside, but for a small square window, the sea and sky are quite abolished. It smells of earth. A visitor from the inconceivable future, I remained there for a short while, imagining what it was to sail the seas in a small boat until one found a faraway island, under a vast sky, where one could build a stone cell in which to pray. Could Ronan, at his most solitary and contemplative, have imagined these times to come? Easier to imagine the kingdom of heaven.

Pixies on motor-scooters, saints in their open boats, shipwreck and quernstones; it was true, I suppose, what someone whispered last night, as we stood in the darkened village waiting for the petrels: "Oh, you can feel your imagination run riot!" Now, in the light of day, I wasn't sure. Imagination, certainly, but not "riot". I crept out from the chapel into the bright day, and spent a little time in the graveyard where more crosses are slowly sinking into the soft earth. To be born and live and die, all in the compass of this little island, always with the sound of the sea, far from anywhere else, what would that do to your imagination? Martin Martin, the 17th-century Gaelic travel writer from whom we glean so much, records one beguiling detail about the Rona people: "They took their surnames from the colours of the sky, rainbow and clouds."

Not riot, because I think places like Rona offer very clear direction to the imagination. The ancient chapel, the village and the long-forsaken lazy-beds are truly poignant, truly evocative of a lost past. We can imagine that past as sweet, as though bathed in bronze light. As I crept around the houses, though, I wondered if such places aren't now offering us pictures of a possible future, too. A remote, changed future, when more once-inhabited places will be abandoned. We can see beginning already floods here, drought there. We may need such images as Rona provides to help us imagine the world to come, because beneath the surf and birds' calls you can hear the long withdrawing roar of human occupation.

Inevitably, the chapel is in need of attention. The south-west corner is badly slewed out of true. The east wall was repaired last century, now the west needs work. The chapel, indeed the whole village, is a scheduled ancient monument. Ironic, in a way, that we've assumed a duty to preserve such places. It's illegal to tamper with them. It's illegal to cause change in these changed places, places that could offer us ways of thinking about change to come.

"Change" is a word you hear all the time from the ornithologists. The petrel-ringing was fun, and faintly ludicrous, but that's how you know when things are in need of repair, when things are slewing out of true. Down on the shore I could see the tall figure of Sarah Wanless, an expert sea-bird ecologist, moving around over the rocks. There had been shags standing there, wings outstretched in their sepulchral way, and now she was looking for shag-pellets. Shags, like owls, bring up what they can't digest, and from their pellets ("like a mixture of earwax and phlegm") Wanless can tell the species and age of the fish they've been eating. It all adds to the picture, increasingly grim, of what's happening in the north Atlantic. Already the birders had made a quick assessment of the numbers of breeding birds on the cliffs, the numbers of eggs they could glimpse at the guillemots' feet, and they were fearful that this year will be another famine year. A collision of over-fishing and climate change has left no sand eels for the puffin and guillemot chicks to eat. Adults are failing to nest, puffin chicks are starving in their burrows. Like MacLeod of old, the naturalists are returning from the Atlantic islands with doleful news.

By afternoon the clouds were a little darker, moving a little more quickly. The sea was taking on the grey colour of a fulmar's back. We would stay another night, though, so there was a chance to explore Rona's northern side, which is a different, harder place. There are cliffs and inlets. The waves surged in with a hollow boom, then retreated in confused turquoise swirls. Guillemots, their backs turned, held their ground on the ledges with nervous fidget and fuss, and I walked along the clifftops a short distance, trying to move carefully - the birders had dinged this into us - so that I didn't panic the birds. If they're frightened, they leave their ledges and fly in great banners out to sea. It's a wonderful spectacle, but in that instant, great black-backed gulls arrive to take the unguarded eggs. Wanless had shown me already a plundered guillemot's egg, broken on the turf. A lovely thing, bigger than you might imagine, deep turquoise with brown blotches. But once it's gone, it's gone, and the bird won't lay another this year.

Then the land falls to sea level, and runs three-quarters of a mile northwards in a peninsula called Fianuis. The rest of Rona is plump and green, but this part is low and narrow. Winter waves can quite inundate it. This is where the seals come every year, a thousand of them, to pup and mate in a great squalor. I liked its ambivalence, its low broken rocks, so I picked my way to the end over grass and thrift and brackish puddles. At the end, where the land disintegrates, a handful of wild geese took to the air. I thought about the sea-birds, and the hard times we've dealt them, and village life and change. Rona, of course, is named for its saint, but later, seized by some inspiration, I asked Love, who speaks a little Gaelic, if he knew what "Fianuis" meant. An outflung peninsula on an abandoned island whose birds are in crisis and whose people are long gone, "Fianuis" means "testimony", or "witness".

The following morning the wind was stronger, and the sea had turned restless and grey. We could see the Poplar Voyager rolling uncomfortably at anchor, just a little offshore. MacLeod's party had to wait seven months, a long Atlantic winter, before they could fashion a new boat of driftwood and wreck and sail home like revenants. Our skipper had other ideas. At about 9am he could wait no longer, so he blew the ship's horn many times, each blast breaking across the island like a storm wave. It was a signal we were expecting. Already we were packing up to leave.

· Kathleen Jamie is the author of Findings (2005), published by Sort Of Books