The Basilica de Bom Jesus, completed in 1605 and current site of the remains of Saint Francis Xavier. (David Parker/Alamy)

You could call it a kind of pilgrimage: a journey through the misty coconut groves at sunrise, just as the holy cows start looking for pastures new.

Each morning, buses and auto-rickshaws heave tourists away from the sugar-soft beaches of India’s Goa state and inland toward Old Goa — the city that was once the seat of Portugal’s eastern empire and that’s still home to more than a dozen Catholic churches, chapels and convents. They’re so close to one another that you could see the lot in one day.

Many people do.

But the true pilgrims visiting Old Goa, in India’s tropical west, have only one church in their sights. And that’s why the Basílica do Bom Jesus, completed in 1605 and gnarled by the baking sun ever since, is often filled to bursting.

Crowds congregate in one darkened corner near the altar, where stone cherubs surround a jewel-studded casket. This glass-sided box is kept so high up that it’s difficult to peek inside. Rock forward onto your tiptoes, though, and you might catch a glimpse of a corpse. The face is a rusty shade of orange and contorted by the passage of too much time. But there’s still flesh on the bones.

Details: Old Goa, India

For the pilgrims who flock here from around the world, and for many Goans, there’s no question: This is the miraculously well-preserved body of Saint Francis Xavier, a Roman Catholic European missionary who died more than 450 years ago. Apart from missing one arm, which is sometimes sent on tour around the world, and one toe (supposedly bitten off by an overzealous worshipper in the 16th century), the Jesuit’s body is surprisingly intact.

Surely it must have been embalmed?

“They scientifically proved that nothing has been done to that body,” one man told me outside the church, smiling proudly. “No chemicals. Nothing.”

At that moment, a woman in a satsuma-colored sari swished past and couldn’t resist joining in. “It’s a miracle,” she said, bobbing her head from side to side.

In November, when the saint’s body will be displayed at ground level for the first time in a decade, believers will be able to take a closer look. The remains will be brought down from their lofty home in the basilica and carried across the road to Old Goa’s cavernous Sé, one of the largest cathedrals in Asia, where they will remain on display for 44 days.

The last time there was an event like this, more than 1 million people came to gaze at the relics. This time, rumors in the Indian press suggest that another Jesuit called Francis — the Pope — could also be in attendance.

The power of Saint Francis

I crossed the road from the basilica to Old Goa’s dusty archeological museum. It wasn’t as crowded as the church, but the galleries were stifling hot. Ancient electric fans pushed the stale air through the former convent, and I soon discovered that by standing completely still and feigning interest in a couple of 13th-century sculptures, I could cool off pretty quickly.

The Portuguese men who ruled Goa for more than 450 years must have had a harder time with the climate. In the museum’s upper gallery, portraits show the bearded viceroys posing in wardrobe after wardrobe of consistently unsuitable clothes, from long socks and frilly neck ruffs to heavily embroidered gowns.

For many Indians, these portly Europeans, who brought their strange fashions and beliefs to Goa, changing the religious landscape in the process, are little more than historical curiosities, people from another place and time. But Francis Xavier, a missionary who arrived in Goa during the early days of Portuguese rule, remains a strangely unifying figure.

“All Goans believe in the power of Saint Francis,” explained Sandy, placing a cold beer in front of me. I’d met the 27-year-old bartender the day before on the beach in Agonda, a two-hour drive south of Old Goa, just as the sun was setting. Eagles spiraled upward on thermals, their wing-tips feeling the air like outstretched fingers, and glassy waves dumped noisily onto the sand. “You know,” he confided, lowering his voice slightly, “I’m a Hindu, and I believe. My friends and family believe in his powers, too.”

I asked why.

“Because you go to Old Goa, and your dreams are fulfilled.”

Magnificence departed

Born at the start of the 16th century in what is now a part of Spain, Francis Xavier was sent to Goa to help restore Christian values, which were declining across the Portuguese colony. It’s said that he performed miracles, converting thousands to Christianity in the process, and then continued traveling east.

In 1552, when he died on an island outside China, he was buried hastily on the beach. It’s said that his body was exhumed several times after that initial burial, as people deliberated over where it should be kept, and every time it was found to be inexplicably intact. News of this strange fact began to spread, and the Society of Jesus ordered that the remains be sent to Old Goa, where they have been ever since.

It’s hard to imagine today, but in 1553, when the body eventually arrived, Old Goa was fast becoming one of the wealthiest and most magnificent cities in all Asia. Stately mansions housed rich traders, church spires scraped the skies, and the population swelled to 200,000. It was as big and as busy as London.

But within 200 years, recurrent outbreaks of malaria and cholera had wreaked havoc, and the city was all but abandoned. Today, only a few of the stone monuments from the city’s heyday still survive, separated by parched lawns and palm trees that rustle gently in the hot air. The place is a UNESCO World Heritage Site, but in parts of town, shriveled nuns are forced to share the roads with tour buses and too many ice-cream sellers, who jostle with one another for customers. “Ice cream!” they shout, at no one in particular. “Possible!”

Whose body is it?

There’s less hustle on Holy Hill, a short walk from the basilica. I followed the hypnotic chirps of birds uphill as wafts of warm coconut oil spilled out from hidden cooking pots. At the Museum of Christian Art, partway along, I found gilt reliquaries, processional banners and ivory carvings — works of art that had been salvaged from some of the city’s old churches. When I left the museum and approached the top of the hill, the remains of a vast, ruined bell tower slowly came into view.

This weed-wrapped complex dedicated to Saint Augustine is the largest of all the religious buildings left to crumble when the Portuguese packed their bags. Broken stones and cracked azulejo tiles still trace the outline of the old convent, and stray dogs keep cool in the shade of cracked chapel walls. Standing alone in the shade of the precarious bell tower, I couldn’t help thinking that if this place were home to a saint — and not just named after one — then perhaps it would still be busy. Or at least still have a roof. People need something to put their faith in.

But even Francis Xavier, the patron saint of this tiny Indian state, has his fair share of detractors. Modern scholars have described him as a misogynist and a racist with little respect for the Indians he so desperately wanted to convert. Others accuse him of ushering in a bloody inquisition that led to the widespread destruction of temples and the torture of non-believers.

And then there are those who say that the whole holy relics thing is made up; that the remains aren’t really those of the saint at all. One theory doing the rounds is that the bones belong to a Buddhist monk from Sri Lanka. It’s claimed that he consumed a special Ayurvedic remedy before his death, which would keep his body intact until the year 4230. Supporters of that theory want a DNA test to prove that the body is that of an Asian, not a European.

None of those discussions seem to bother locals. Worshippers were still flooding into the Basílica do Bom Jesus as I left Old Goa for a final day on the coast. And by the time I reached Agonda’s beach, passing tiny temples and churches along the way, the basilica’s crowds were a fading memory. Warm waves kept sloshing at the sand, and tourists strolled along the shoreline holding hands. The same cows that had seemed so sprightly in the cool of the early morning now fanned themselves with lazy tails, chewing serenely at the cud. And all the while, the eagles kept circling.

As the birds climbed higher and the sun sank ever lower, one thing felt certain. As long as there are places like this — and for as long as the mystery of Saint Francis Xavier continues — the pilgrims will keep on coming.

Vickers is a freelance journalist and guidebook author based in Sweden. Follow him on Twitter at @StevenJVickers or visit his Web site,