An expedition ship takes Peter Heller into remotest Indonesia—and gives him one awe-inspiring experience after another.

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Credit: Bruno Cazarini

The Black Zodiac skimmed fast over blue water. The bow skipped and pounded into the light swell and threw back spray, aiming for a small green island floating low on the sea. From the island, a long dock. The inflatable bumped into it, and my wife, Kim, and I clambered out and trotted to the deep shade of the trees. The path led straight to the edge of a jade-green lake, rimmed with dense forest. Exuberant birdcalls rang out over the water. Already the morning was abundant with two ingredients of certain happiness—delicious coffee at dawn, and a wild body of water to swim in. I thought: It can’t get any better than this. I was wrong.

Because the lake was not just any lake; it was in the middle of a coral atoll called Kakaban, at the head of the Makassar Strait, 40 miles off the east coast of Borneo. And because it had taken us nine days and 2,000 nautical miles to get here, sailing from Darwin, Australia, on the Silversea Cruises’ Silver Discoverer expedition ship. And, most of all, because the lagoon is one of the very strangest places on the planet.

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We put on masks and snorkels and slipped into warm water and it was hard at first to stay calm. Pulsing all around us were thousands upon thousands of orange jellyfish. They were the size of small human hearts. We lay motionless as the throbbing, velvety domes bumped our legs, our arms, our ears. Stingless and benign. As each jellyfish beat its translucent, yolk-like mass to a similar tempo, we began to feel like we were floating in a soundless music, as if we were suspended in some kind of jellyfish heaven. Tiny, transparent needlefish swam back and forth in front of our masks. Kim squeezed my hand and stuck her head into air and took out the snorkel. “Hey!” she said. “I have a confession: I kissed one on the lips!”

I said,“I’m jealous.”Then paused. “How did you even know where its lips are?” She made a face and went back under.

When our fingertips had turned to raisins, we climbed out and ran up the boardwalk and back through the rain forest to the island’s outer shore, where we swam out to the edge of the reef. We dove down into clouds of fish. A large green sea turtle glided by, curious, just beyond our reach.

This was a trip I had always wanted to make: traveling from Australia to Borneo, up through the Malay Archipelago—threading Indonesia’s 18,000 islands, straight into the heart of the Coral Triangle, one of the world’s epicenters of marine diversity. I’m a veteran adventurer who has spent far too many nights sleeping on the ground, and I never imagined making the journey on a luxury expedition ship.

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“Luxury” means that the Silver Discoverer was outfitted for 120 passengers and 96 crew—a pretty good ratio. It also means “all-inclusive,” with a sommelier to help pair wines with your meals, and lectures by experts on everything from Indonesian weaving to how fish talk to one another. (No kidding.) Sweetest of all to me, someone who adores good coffee, was that every morning at daybreak there was a double tap at our cabin door by the butler, Georgin, who delivered a carafe of Indonesian dark roast and two flat whites. Kim and I would sip the coffee on our balcony while the breeze blew the curtains and a molten sun rose like a burning ship lifting from the horizon. The Silver Discoverer has a library, a lounge, and a back deck with a swimming pool, from which one can order exotic coffees or cocktails at almost any time of day or night. But our own little balcony was the most marvelous, especially at dawn.

“Expedition” means that the ship is smaller and more agile than the big cruise ships I often see, and can get close to the smallest islands and dock at barely-mapped ports. What the ship does not have is a casino and miniature golf. What it does have: a fleet of a dozen fast Zodiacs that are always ready to deploy for close-up exploration. Plus a team of world-class naturalists and divers to help you ID birds and fish and geologic features. It’s rough-and-ready matched with real elegance.

That magical morning, after hours in the water, we ate a lunch of roast pork and virgin mojitos on the aft pool deck. We shared the meal with a theater critic from London and a children’s book author from Australia. The Brit described how he had developed a passion for monkeys, almost an obsession. It was part of the reason he was on this trip, he said. The dessert was my favorite, strawberry panna cotta, and I thought: I could get used to this.

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Credit: Bruno Cazarini

What I could not get used to was where we had been in the last 10 days. The best travel always seems at some point like a dream, but this was going beyond surreal. Had we really docked in Sulawesi, the great scorpion-shaped island east of Borneo, and ventured up into the western mountains to Tana Toraja, home of “the culture of the dead"? The people there live in palm groves among the rice paddies in tall, boat-shaped houses with high prows at either end, and save up all their lives for funerals. These can involve up to 80 sacrificial water buffalo—each of which can cost thousands of dollars—as well as temporary funeral houses (as large as homes in the village) and tau tau, life-size carved-wood statues of their ancestors. Of course, when a grandmother dies, no one can afford all this right away, so the family hires someone to embalm her with formalin and herbs and prop her in the kids’ room where she can be “sick” for many years; a child offers her meals three times a day and asks, “Tea, Grandma?” and no one is bothered that she never answers or eats.

In early evening, as the low sun lit the lush and jagged limestone ridges and turned the rice paddies a tender, brilliant green, we walked among one of these temporary villages, and saw the wide-eyed tau tau looking down from the cliffs, along with skulls lining the ledges. We passed a living burial tree where deceased infants are interred in carved holes so the tree will grow over and around them. And on the way home we stopped at a funeral in its seventh day; the black-clad relatives had the dogged look of fans at a 12-inning baseball game, and we had to step around the pools of blood of unfortunate buffalo.

Maybe even more startling was the whaling village of Lamalera on the Savu Sea. Georgin had knocked, as usual, at dawn. He spread a tablecloth and laid out coffee, fresh croissants, and eggs Benedict. Georgin is from Mumbai. He has a bright smile and a sweet nature but an uncertain future, because he is addicted to Breaking Bad and has only three episodes left. I took the espresso out to the balcony and blinked. A volcanic mountain rose out of the mist. Green and rugged, it floated on the smooth sea like a fairy-tale island. Could it be that there are still places on the planet this remote?

Clinging to the edge of a rocky cove was a cluster of small houses, a pastel-blue chapel, a line of thatched-roof huts from which stuck the prows of wooden longboats. Later we piled into Zodiacs and landed on the sand. In front of the boathouses, crews sat cross-legged before their outrigger canoes—12 to 14 men per boat—and greeted us shyly as they smoked. They were whalers. When a lookout on the point spotted a whale spout, the men ran the boats down to the water and leaped in and paddled, and raised a sail made of woven palms. They gave us a demo. They slid their boats to the sea. They sang as they rowed. Amazing that they hunted sperm whales from such slender craft. When they got close enough, a harpooner on the bowsprit leaped whaleward and threw a spear as he fell. He might land on the back of the whale, who sometimes killed the man and wrecked the boat. In the chapel back in town, the statue of Jesus held a harpoon.

I am not in favor of whaling, but these villagers have zero flat ground for farming, and they trade the meat for vegetables from a village inland. It is a subsistence-and-barter economy—very rare in 2015. Only one other ship had stopped in to visit them in the past five years. However one feels about their practice, it was a remarkable anachronism to witness.

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Kim and I sleep beautifully on ships. Something about the roll and the wash of the waves through the open door lulls us into deep slumber. The next week would bring more scenes that might have come straight from our dreams. In Borneo, on launches up the wild Kinabatangan River, we saw proboscis monkeys jumping from tree to tree, and places where pygmy elephants had trampled the bank, and brilliant hornbills, and storm storks, and kingfishers the color of wild roses beating fast upriver. One night we stood on our balcony and got drenched in a squall that drove the rain sideways and laced the sky with lightning from horizon to horizon. As fast as it had come it cleared, and the Southern Cross hung over a placid sea.

At a Dayak village, up the Kayan River, we shook the hands of about 100 villagers in a long line, many of whom wore beadwork and weavings with headhunter motifs. At the Sepilok Orangutan Rehabilitation Center, above Sandakan in the Malaysian part of Borneo, Kim and I were fascinated by a wild young male who bent the smaller trees and swung from one to the next, getting closer and closer. Fascinated—until we realized he was stalking us and the guide yelled, “Run! Run!” I was sorry the monkey-loving theater critic was nowhere in sight.

In the Makassar Strait, though, on the afternoon of our long sojourn with jellyfish and turtles, we all gathered on the aft deck for an equator-crossing ceremony. Someone shouted, “Look!” To the west, against the sun, we saw hundreds of spinner dolphins, porpoising through a boil of tuna. The dolphins leaped from the sea and spun in the air, throwing shards of silver into the sky. Overhead, scores of frigate birds circled on bent wings. I reached for my wife and held her hand. A piece of the world still worked. In this far sea, it held a beauty beyond reckoning.

14-night cruises through Indonesia from $9,950 per person, double, all-inclusive.