Secret beaches and chocolate hills: This cruise is packed with adventures

Yuri is at the tiller of our zodiac as we putter in for a dry landing on Sibuyan Island, Philippines. Our expedition leader is Thijs Holkers, and he briefs us about the trek that is just ahead. "It's a jungle hike about 40 minutess, a few shallow river crossings, then a beautiful waterfall swim." We shoulder daypacks and set off with local guides and several uniformed Philippines soldiers, who are cheerful and happy to help.

At Dagubdub Falls, our group of 40 sweaty hikers slides in for a freshwater swim. But when Filipino youngsters set a table for us with chilled bottles of coconut and strawberry lassis, I feel myself squirm: older, wealthy white people, attended by less-privileged brown people. It's a fact of most cruise trips, and while I'm in no position to be indignant, I have to acknowledge the playing field we're on.

I'm on Heritage Expeditions' inaugural cruise from Manila to Darwin on the small-ship, 140-passenger Heritage Adventurer, through the remote islands of the Philippines and Indonesia, and so is operations director Nathan Russ, son of company founder (in 1985) Rodney Russ. Theirs is a small company, based in Christchurch, with just two ships; the other is an expedition yacht, the 18-guest Heritage Explorer. A company this size needs to be highly attuned to client feedback, and over the next 12 days, Nathan will see for himself what works and what doesn't. Caroline, a fellow passenger and expedition cruise veteran, expresses a feeling that's already common among my shipmates: "It's sensible to start in Manila, the ship has to be resupplied, but I was excited about jungles and corals and birds. Not so much, a city tour of museums and monuments."

That night, Thijs judges it too rough to snorkel near the ship's anchoring by Cresta De Gallo Island, so we're champing at the bit for our morning on Ticao Island, Philippines.

About 8am on day three we motor into a crunchy sand-coral beach for our much-anticipated first snorkel. The 29-degree water and 30-metre visibility are the sorts of reasons you join an expedition cruise, and Caroline can't stop smiling. The sheer variety of corals we see is staggering, from hard (plate, cabbage, boulder, staghorn) to soft feather-stars and anemones, the latter inhabited by families of bright orange or deep mauve clownfish. Juvenile black-tip reef sharks, 70-centimetres long, flit about the sandy shallows.

The next day is a particular joy for photographers and wildlife enthusiasts, as we board tour buses on the Philippines island of Bohol to visit its Chocolate Hills (hundreds of perfect breast-like brown hillocks) and resident tarsiers - the world's smallest primate, a fist-sized tree-dwelling marsupial with huge eyes and beautiful long fingers that enable it to cling sleepily to trees in the daytime. Evolution has barely touched this nocturnal animal in 45 million years, making it one of the "oldest" primates on earth.

At Bucas Grande Island, our last stop before we'll swap Philippines shore passes for Indonesian visas, we hop into locals' outrigger canoes and explore the maze of jungle-covered "mushroom" islands. The surrounding seawater is eerily green and placid, also soupy with harmless jellyfish, which we jump in to view. Suddenly it's raining the way it does in the tropics, like swimming pools falling from the sky. "Welcome to the jungle," I murmur to myself, face upturned and smiling, T-shirt soaked through.

In Indonesia now, anchored at the northern end of Sulawesi, we visit Tangkoko National Park, where encounters with black-crested macaques, tarsiers and knobbed hornbills are our rewards for a sweaty, guided jungle trek - a trip highlight, judging by the excited jabbering over dinner.

Passengers on an expedition cruise typically have their primary area of interest: reefs, birds, animals, photography. We're lucky to have British filmmaker Neil Nightingale on board, talking about his filming for various BBC wildlife series, even his work with Sir David Attenborough. Neil discusses 19th-century British naturalist Alfred Russel Wallace, and makes sense of our route, east of the "Wallace Line" - it reflects Wallace's thoughts on how geographical separation leads to different genetic traits between otherwise similar animals. "His 1858 letter to Charles Darwin on the subject of evolution had Darwin get a wriggle-on and publish his 1859 book, On the Origin of Species," Neil says.

Wallace's own book, The Malay Archipelago, published in 1869, remains one of the most influential about the region and has never been out of print.

It's midway through the trip and we're familiar with the daily drill of lifejackets and zodiac landings. At Seho Island, soft corals abound, including one feature I've never seen before - a single anemone, at least a metre square, but with multiple resident adult clownfish instead of the usual pair. And another, this time with at least a dozen tiny juvenile clownfish hovering amid its poisonous tentacles.

No cruise ship has ever visited neighbouring Taliabu Island, where a procession of cheering people and revving becak - the motor-cycle-powered, rickshaw-style conveyance we'll each be boarding - greets us. As we rumble single file past the ramshackle market in Bobong township, I find myself waving to the crowds and thinking, this must be what King Charles has had to do his entire life.

There are a few minutes of sanity when we stop to watch a section of sago palm being pounded and strained to make starch; I find myself quietly applauding the human ingenuity to extract carbohydrate by almost any means. Then we're celebrities again, during an official town welcome that includes gifts and speeches.

Heritage Adventurer is also the only cruise ship ever to visit Buru Island (2022 and 2023). Photos of Buru belong on postcards, because this is just what a tropical island should look like: cloud-shrouded mountainous interior; thick emerald-green jungle; gin-clear ocean surrounds. King Kong would make himself a respectable home here. The village welcome features the usual excited demand for selfies, before eight teenage girls gather for a traditional dance. All are dressed in tight headscarves, ankle-length skirts, long-sleeve blouses. At 10am on a tropical island. Village blokes are in singlets and shorts, some smoking; a reminder that wherever religious dogma holds sway, it's coincidentally convenient to be a man.

I'm reflecting on this injustice just as the local men start to toss crumpled rupiah notes at the feet of the demur dancing girls. I check the feet beneath the over-elaborate dress - all Nike, Adidas, Converse, sneakers. Teenagers, it seems, will be teenagers.

A 10-minute boat ride away is the village of Pasir Putih. After a precarious ladder-climb and wander around, I'm gobsmacked by the hundreds of bright-painted houses that perch precariously on stilts over the sea. The cleared hillside behind would be too steep to build on, so this seems like an imaginative workaround.

Our final two days include one last snorkel session, a dive site where, in 1988, Gunung Api ("Fire Mountain") erupted, and the ensuing lava flow swallowed part of the surrounding reef. Regrown staghorn corals tinged olive-green and cabbage corals are everywhere. There's an enormous garden of some "columnar" coral type I can't identify and fish varieties I've never seen before. We spend 90 minutes in the sea here, but we could have snorkelled it every day for a month.

A final presentation in the ship's lounge from Neil, alongside partner and fellow wildlife film-maker Karen Bass, is a riveting account of the advances they've seen in equipment and technology, from drone cameras to on-site editing software.

It feels like a lifetime's worth of experiences I have to reflect on as I curl up for our overnight sailing to Darwin. You finish an expedition cruise exhausted, elated, fascinated by the world around you, and with a hundred more questions than when you started. It's answered a few of Nathan Russ's, too.

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THE SHIP: Heritage Expeditions' Heritage Adventurer

THE SIZE: 124 metres long, 82 cabins, 140 guests

GOOD TO KNOW: The tour starts in Manila with an overnight stay in a hotel and a group dinner. Next morning, after breakfast, a charter flight transfers the group to the Philippines city of Legazpi, where the ship departs in the evening.

GET ON BOARD: Undiscovered Philippines & Indonesia is scheduled for June 22 to July 5; its 14-day itinerary (Manila-Darwin) does not include airfares, but does include the Manila hotel, dinner and breakfast, and the charter flight from Manila to Legazpi. For 2024, a day-tour of Manila has been replaced by a visit to Mayon Volcano National Park, near Legazpi city, while two new island destinations will substitute for two others.

HOW MUCH: Fares from $14,350 a person triple-share, to $29,000 per person for a suite.

EXPLORE MORE: heritage-expeditions.com

The writer was a guest of Heritage Expeditions.