The clear blue underwater space around us stretched to infinity—the visibility must have exceeded 100 feet. Clouds of fish hovered above, between, and behind the exquisite coral. These waters off Pulau Kri have one of the world’s richest coral communities. Green, red, yellow, and purple, the coral covers the slanting bottom in mushrooming plates, circles, antlers branching like trees, and frilly lace. It wasn’t all dreamy beauty, though. A lightning-fast strike of a shark on a hapless grunt scattered schools of minnows. But they soon settled back into the magical waterscape.

Hengki Kolit, our translator, guide, and friend aboard Whale Song, our 94-foot expedition motoryacht on the way westward from Papua New Guinea, pointed us to Raja Ampat—a region off Irian Jaya in the Indonesian islands fabled by world-wise scuba divers. Besides offering diving grounds, Raja Ampat’s main island, Waigeo, gave us our last chance of seeing the dance of the birds-of-paradise. Kornelius, an experienced tracker from the nearby village of Kaboei, piloted our tender through shady creeks to a steep bank of dense woods. Sweaty and muddy, slipping and sliding, we climbed to the lek where the birds display. As slow walkers, we missed the best time, which is just after dawn. Still hoping, Kornelius set off a concert of whistles—cooing, screeching, and hollow gurgling—all confirmed by unseen distant calls. A bird swung by, bright blue coverlets, orange legs and white chest, the size of a large raptor, but actually just an imperial pigeon. Then it started to drizzle, and birds-of-paradise definitely don’t dance in the rain.

Returning a different way we passed a large hull under construction, which was almost ready for launching from a cradle of saplings. Wooden boatbuilding in Indonesia continues in the old tradition with hardwood pegs holding planks to the frames. Some of these pinisi cargo carriers are up to 100 feet long. And fishing bagans, wide and spidery with outriggers on both sides, can be massive, too.

We steered southward, convinced that we had already seen the best reefs. Wrong! An archipelago of smaller islands spreads southeast from Misool. Tempted by the pillar rocks off our anchorage at Pulau Wagmap we splashed in. Underwater, the pillar shapes continued, wrapped with sponges, hard corals, and soft corals, pliable and gaudy. In the slight current of the dropoff, the fuzzy soft coral trembled, teeming with fish life. We swam upside down through a cathedral-like arch bursting with color, a giant Napoleon wrasse keeping station near us. This was truly the best dive of the voyage, and maybe of my life.

Vibrant, Volcanic Indonesia

Indonesia includes thousands of islands with only the largest populated. Various ethnic groups live on these islands, each with its own language and religion. Today all can speak the unifying Bahasa Indonesia lingua franca, but tensions often surface. On Seram Island, Whale Song anchored off Sawai, a village where both Christians and Muslims live. The port captain in military garb arrived on board to see our papers and collect a port fee (with no receipt offered), while surreptitiously asking for alcohol. The fishermen in canoes came with gifts of bananas and papayas. They offered to fish near us all night to protect us from robbers. After a peaceful night we visited Saleman, a village across the water. One dirt road runs along the shore by three densely wooded mountains, all over 5,000 feet. The shiny dome of a mosque rose over thatch roofs, a huge slit drum outside the door to beat at prayer time. Children paddled in from school in outriggers. A man climbed a coconut palm and dropped green drinking coconuts to us. The kids surrounded us, all smiles, practicing their English. Only some of the girls had covered their hair—this village, too, was home to both Muslims and Christians.

Our visit to Bandaneira in the Banda Islands was tranquil, too—long forgotten was the bloody clash between religious factions in 1999 that exploded in Ambon on Pulau Seram to the north and spread south to Banda. Whale Song lay to anchor with stern warps on the shore of Gunung Api, a soaring volcanic cone. Across the bay, the waterfront and town hummed. From the 17th to 19th centuries this was the center of the fabulously profitable shipments of nutmeg believed to be a potent cure for the pestilences of medieval Europe. The shipments of nutmeg and clove, first in Portuguese hands and then Dutch, turned the Netherlands into a major power. The behemoth of the 1611 Dutch fortress still overlooks the throngs milling in a local market, where we had the first taste of the legendary durian fruit. Its reputedly revolting smell was more like slightly rotten fruit, and the custardy pulp inside tasted vaguely of boiled sweet onions.

In February, March, and well into April the winds laid low, variable and light. From Banda onward we levitated over an ocean of polished silver, a mirror for the clouds towering over islands ahead. This was a volcano alley—distant black mounds on the horizon slowly rose into smoking pyramids. The calm weather helped, and we often anchored in water over 100 feet deep on slopes from reefs fringing the volcanoes. At Manuk Island we plunged into water swarming with sea snakes. Deadly venomous but with mouths too small to bite, the curious snakes would nose our wet suits and swing away. I’m not sure how much they liked living in the sea because they often climbed our anchor chain to curl up on the warm foredeck. Hundreds of boobies and frigate birds circled overhead. These were a unique sight as traditional egging has wiped out most colonies on the inhabited islands.

Volcanoes in this part of Indonesia can erupt any time. Gunung Api, hovering over our anchorage, has killed people, the last time in 1988. Pulau Serua, a night stop on our route, smoked heavily. Green vegetation has reclaimed Pulau Nila’s peak but earthquakes often rattle this place. Pulau Damar puffed smoke from sulfur-rimmed ulcers that pockmarked a bare hillside. In the anchorage, a fisherman in his canoe, his village ghostly in the yellow volcanic haze, sold us a tuna-like fish, striped as a rainbow. He prepared to fish all night in the glare of our lights. He rigged his line with a round stone from a heap at his feet, wrapped around it the flank of a fish containing a hidden hook, and then camouflaged the whole lot with a large leaf. On anchor watch at 2 a.m. (we kept night watches due to changing currents and uncertain bottom), I saw him pull in the line and lean back for a snooze, the canoe still empty.

Volcanoes thousands of feet high continued to dominate the scenery as we swung more west. On larger islands numerous villages attracted to the rich volcanic soils clung to smoking slopes, existing with the ever-present threat of an eruption and the monstrous waves that often follow. Our guide and translator, Hengki Kolit, lives in Maumere on Flores Island, fortunately on high ground across from the Rokatenda volcano. In 1992 the earth shook, the sea heaved up 60 feet, and 2,500 people died.

Volcanoes also towered on the great island of Lembata, their heads vanishing in clouds of ash. After reading Tim Severin’s In Search of Moby Dick, I knew we just had to stop at Lamalera, a village teetering on the edge of Lembata’s south shore. A row of peaked thatched roofs on the crescent of the beach shaded double-ended boats. Bamboo spars, harpoon shafts, and rolls of woven-mat sails rested on the thwarts. The sail shape looked as if it came from an engraving of an 18th-century expedition. The last time I saw a similarly shaped hull was in the Nantucket Whaling Museum—not surprising since Lamalera’s villagers live off whaling, the sperm whale their preferred target. Venturing offshore under sail, totally engineless, the men give slow chase with oars. When close in, the harpooner balances on the bow platform and flings himself, harpoon in his hands, into the sea to add more power to the iron planted in the animal. Lamalerans don’t kill baleen whales since their legendary ancestors arrived here on the back of a blue whale.

Whaling History

Today whaling in Indonesia is often viewed with horror by outsiders. However, in Lamalera the annual take may be only 20 animals, sometimes none. In the 1970s the World Food and Agriculture Organization sent in a Norwegian with a powered boat to show the village how to catch more whales. His success overwhelmed the rural economy, the barter value of the catch declined, and the villagers suffered while carcasses rotted on shore—a lesson not to upset the traditional sustainable economy of remote places.

The terraced streets of Lamalera cut into a steep mountain hill. Over fences made of whale bones I could see women weaving ikats, fabrics celebrated among folk-art followers. From up the road came the sound of banging: a new boat under construction. A wiry shipwright with an adze was hewing slabs of timber into precisely fitting notched planks; aside two elderly men chiseled wooden pegs for plank fasteners. They would insert the ribs later, each lashed to stubs carved by adze on the inside of the planking. The visit to Lamalera took us back centuries.

Natural Wonders

Indonesia suffers from extreme population density. The country’s 260 million people span 6,000 islands, but the majority live on just three: Java, Bali, and Sumatra. Bali was both a delight and instructive nightmare. For yachts, Benoa, the main harbor, has a marina—the first and the only one we saw. A short drive away lies Ubud, an ancient town of tightly stitched villages, temples to the Balenese Hindu gods, the sacred Monkey Forest, and ancient burial grounds. The earth of the burial grounds is recycled when cadavers are exhumed for bone cleaning, final cremation, and disposal in the sea. Fanged moss-green monsters and statues of female warriors with clubs, their bulging eyes furious, guard family compounds. The drive to Ubud calls for nerves of steel. Throngs on motorbikes join the free-for-all road madness, racing left, right, and against the traffic stream, blissfully ignoring rules and the likelihood of broken necks.

As Whale Song headed along the east coast of Bali, which is dominated by volcanic Gunung Agung, tourists vanished as black grit and gravel replaced sandy beaches. Hundreds, if not thousands, of graceful outriggers straddled every flat piece of the shore. At dawn they would launch into fish-rich seas where the Indian Ocean, loaded with nutrients, pushes north into the western Pacific.

Besides the riches underwater, the islands have some other startling wildlife. If you fancy a brush with man-eaters, head for Komodo National Park. After diving with grand manta rays, which banked through blizzards of plankton, we anchored inside the deep Rinca Island Channel with its five-knot currents. At dawn a movement on the beach caught my eye—a lizard-shaped Komodo dragon, about nine feet long, its head swinging, foraging. Faced with such a photo op we rushed the dinghy in and grounded in the shallows. The beast, alerted, flicked its forked tongue toward us, tasting. Were we young, tender, edible? He then marched straight into the sea. Komodo dragons may not dive but they easily swim—the good old Yamaha hadn’t run so fast in a long time.

In recent years yachts have been flocking to Tanjung Puting National Park abutting the Kumai River and port on the south coast of Borneo/Kalimantan. In the park’s nature reserve, we humans could hobnob with orangutans, our distant relatives. Camp Leakey was established by Dr. Biruté Mary Galdikas, a Canadian primate researcher, to take care of abused or abandoned pet apes. But in a short time, totally wild orangutans from the deep forest discovered the handouts of choice bananas. To reach the place hidden in the bewildering maze of creeks, our yacht’s owner chartered a klotok, a roofed wooden boat, with crew, a cook, a guide, and mosquito nets to sleep under for two nights. Off the main tributary we slipped into a tunnel of a flooded forest. The scene turned wild; our captain swerved around two proboscis monkeys doing the breaststroke across the stream. Other monkeys were flying between trees. Loud grackling calls above revealed a couple of startlingly shaped hornbills on the wing. In the forest “orang” infants draped over their mothers as they all rode down trees and indulged in upper-level acrobatics to our delight.

The immense area of Indonesia includes some 17,500 islands. Thanks to complex geography, this enormous wild territory and its ocean remain open to those who seek a natural, less-developed world. And visits to populated centers add thrills and the surprises of different cultures. On the way westward down river from the last stop in Indonesia in Pontianak, Borneo, the bow plowed a muddy furrow for 10 miles to the blue sea as we discussed coming back to see places we missed.