Sidotti helped shaped Japan's view of the Western world with his knowledge after he won over the nation's leading scholar of the day, historians say. But he fell from grace after refusing to give up his faith and his final days and death have been shrouded in mystery.
Christian missionaries made aggressive inroads in Japan in the 16th and 17th centuries, gaining adherents among commoners and even powerful warlords.
But fears they were an advance guard for European colonialism spurred a brutal crackdown long before Sidotti arrived.
- Human jigsaw puzzles -
Three sets of bones were unearthed in July 2014 from land that now forms the parking lot of an upscale condominium but was once the site of the prison -- the Kirishitan Yashiki, or Christian Mansion. Its only reminder today is a stone marker commemorating the spot.
National Museum of Nature and Science researchers near Tokyo carefully cleaned the skeletal fragments before piecing them together like human jigsaw puzzles in a painstaking process that took more than six months.
Kenichi Shinoda, the museum's chief of anthropology, analysed DNA from a tooth and concluded that one of them had the same genetic type as present day Italians.
Japan's historical records show that only two missionaries from Italy had been held at the site, Sidotti and Giuseppe Chiara.
The latter was the model for the main character of a Portuguese priest in late Japanese author Shusaku Endo's novel "Silence," which director Martin Scorsese is turning into an upcoming film.
As records show that Chiara was cremated after his death at 84, the unearthed remains are almost certain to be of Sidotti, who was 47 when he died in 1714, researchers said.
While detained at the prison, Japanese Christians and foreign missionaries were tormented with demands they renounce the banned religion -- many did so under duress.
- 'Changed Japan' -
While they feared foreign religion, Japanese officials also craved Western knowledge and scientific insights harder to obtain under the official policy of national seclusion from 1639.
As part of his interrogations, Sidotti was questioned by Japan's top Confucian scholar, who developed a deep respect for the Roman Catholic priest for his knowledge of geography, languages and global affairs, experts in this case explained.
The scholar, the renowned Arai Hakuseki, is said to have tried to help Sidotti but the priest was later sent to the dungeon amid allegations he baptised the Japanese couple tending to his daily needs.
The Italian died there, but it is not clear exactly how, researchers said.
Historical accounts, such as those written by Japanese scholar Mamiya Kotonobu about a century later, however mention that Sidotti was accorded a certain respect and treated far better than other prisoners -- even i ndeath.
Researchers say that is backed up by evidence from the remains.
"His body was laid flat in a casket, a luxurious one as far as I can tell by the brackets," Akio Tanigawa, professor of archaeology at Tokyo's Waseda University and lead researcher on the remains, told AFP, referring to coffin pieces discovered with the bones.
"People did not bury human bodies like this," Tanigawa stressed, suggesting Sidotti was likely given a burial "in the Christian way".
He said that in 18th century Tokyo, then known as Edo, people were buried in a sitting up position in a small tub.
The two sets of bones unearthed next to Sidotti's may be those of the Japanese couple, Chosuke and Haru, researchers said, as at least one was placed in a small tub, the then traditional way of burial.
The missionary had a great impact on Japan, Tanigawa stressed, citing books by Arai. An adviser to the rulers of the time, he penned a study of the Western world for which Sidotti is cited as a key source.
Tanigawa explained: "The knowledge shared by Sidotti surely changed Japan's view of the world."