Yin Nean’s lightly pencilled handwriting is the code that unlocks Cambodia’s two most important genocide archives. At the Documentation Center of Cambodia (DC-Cam), he has helped with the collection of 600,000 Khmer Rouge documents, and transferred the fragile paper archives onto microfilm.

At the Tuol Sleng Genocide Museum, he stands with families as they find photos of murdered relatives. He has helped excavate a mass grave, conducted interviews that led to the revelation that 179 prisoners escaped death at Tuol Sleng, and was a member of a volleyball squad that used to train inside the old prison compound.

But now, after 34 years, 56-year-old Nean has announced his retirement. It has come as a shock to those who know him, especially to DC-Cam’s executive director, Youk Chhang.

“Individuals, researchers, former Khmer Rouge victims ... he works with all kinds of people in the world and none of us ever sent him a thank you card,” said Youk, sitting in his DC-Cam office this week. “I want to cry when I think about this. He always smiles, he never complains.”

Nean is a man of many letters but few words. Unlocking one of the upstairs rooms at Tuol Sleng on Tuesday, he refuses the offer of a chair and squeezes his bulk behind a child-sized desk instead, where he shifts uncomfortably.

He has never been interviewed before, and discussing his life does not come naturally. “I was hungry,” he says of life under the Khmer Rouge, “I was happy,” of his promotion to senior archivist. But Nean knows that his story is an unusual one.

His first job at Tuol Sleng was as a cleaner. It was in 1982, only three years after the Khmer Rouge fell to Vietnamese-backed forces.

In 1979, the execution centre known as S-21 had been hastily scrubbed down, the remaining bodies of prisoners burned as a sanitary precaution, and the buildings of the repurposed school opened to international visitors.

The documents that would go on to form the precious archive of prisoner biographies and confessions had been found scattered around the courtyard, some half-burned by Khmer Rouge cadres before they fled.

Nean didn’t think much of his new workplace. “It was dark and smelled of blood, and the torture equipment was still there,” he recalled on Tuesday. “I got goosebumps when I went into the rooms alone.”

In lieu of salary, he was paid in rice, oil, sugar and cigarettes. The climb from casual labourer to skilled technician was a slow one: after a few years he secured a salary, then a promotion from cleaner to guard. Once the Vietnamese left Cambodia in 1989, he was hired to the archive room, and received some training from the Ministry of Culture.

His break came in 1995. The young Youk Chhang, then program officer for Yale’s Cambodian Genocide Program, had just convinced the university’s finance department to keep funding the field office’s work tracking down Khmer Rouge documents, which Youk insisted were still turning up “used as wrappings for fried bananas in the local market”.

He secured a grant of $25 a month to hire an assistant, and chose Nean. It was the start of what Youk describes as “a real friendship”, and a working relationship that strengthened the following year, when DC-Cam became an autonomous body.

“Cambodia is a country where trust has been broken, but through this horror we have found something,” Youk said. There are parallels in the two men’s life stories.

They are almost exactly the same age, Youk thinks he is the “big brother” by a small margin, and both were separated from their families by the Khmer Rouge and assigned to mobile work units digging canals. Both men were sent to Battambang province, Youk immediately and Nean after three years in Prey Veng.

At the end of the regime, their paths diverged. Nean spoke no English or French, and heavy US bombing in Prey Veng had disrupted his education long before 1975. He returned to his family’s land until his uncle secured him the job as a cleaner at Tuol Sleng.

Youk, who was bought up in a middle-class Phnom Penh family, worked for international organisations in the capital, and spent time in the US. Passion, and a natural media savvy, propelled him to the top: in 2007, Senator John Kerry selected him as a Time 100 personality, under the “heroes and pioneers” category.

The two men’s collaboration has hinged on what Youk terms a shared ability to “read history as art”.

When working together, they navigate the archives using visual prompts – “the one with yellow pages, it has some pictures and the paper is very rotten” – rather than serial numbers.

“I’ve been doing this for him for 20 years, and he’s never missed a request,” Youk said.

Nean’s education in the nuances of archiving has relied on an innate resourcefulness. He has received training abroad – but not in a language he can understand.

In the early 1990s, he was sent to the US to pick up a microfilm machine used to produce replicates of the Khmer Rouge documents in the archives. Nean assembled and operated the machine using a manual only available in English. “I prefer practice to lectures,” he comments, with characteristic understatement.

Nean’s contribution is recognised by those who have worked with him: a “key player” in preserving documents via microfiche, according to Craig Etcheson, author of After the Killing Fields, and the man who “quietly and professionally secured and maintained the most damning empirical records of the Khmer Rouge era” for Peter Maguire, author of Facing Death in Cambodia.

When his personality is mentioned, it’s in the context of his silent dedication: “A quiet soul with a charismatic smile in his eye,” says Theresa de Langis, who is using the archives to research forced marriages. “I was speechless when he showed me the confessions, the registry handwritten, point by point, in his hand.”

Nean is a hard man to draw on the true horror held in the archives. When he saw S-21 commander Comrade Duch on trial in 2009, he noted simply that he was “willing to work and check everything before sending it out – really well organised”.

But there are moments when the neatly numbered documents become something more real, particularly when families come looking for their relatives.

He recalls one story with rare emotion: parents who came to view the file on their son who had died at Tuol Sleng, and discovered that the man who killed him had been a family friend. Nean gave them a copy of the photo so they could conduct a proper funeral.

For several years now, Nean has been trying to write a book. It will be part history and part personal memoir of Nean’s time at the archives. Youk’s advice: read the Khmer translation of David Chandler’s Voices from S-21, and “write the things that are not in it”.

What that means, often, is ghosts: rumours whispered in the corridors, like the guard a decade back who died of a heart attack after sharing a dream of spirits at the old torture facility with three companions.

The day after we meet at Tuol Sleng, Nean stops by Youk’s office in DC-Cam on his lunch break. He giggles nervously as Youk tries to question him. “Do you regret doing this work when you’re not well paid?” he asks. “Why are you retiring? What do you look forward to when you get to work?”

Nean’s answers are quiet and short. He loves his job, and has little interest in Tuol Sleng outside of the archive room – an answer that makes Youk cackle with laughter.

When Nean says he is not worried about retiring because the new, younger archivists are university educated and have trained in Vietnam for a month so will be good at their jobs, Youk reprimands him: “You have trained for 34 years!”

In a more reflective mood, Youk explains: “Technology cannot replace history. We think that digitisation will serve our interest but only in the short term. History remains with its own way telling stories and communicating. For me, this man is history.”

“He’s like the seven-headed dragon who protects the Buddha,” he says. Nean laughs off the comparison. His work has made him happy, he says, but he wants to focus on his book. His first grandchild has just been born, which makes him feel old.

“All of my friends are already retired, and I think maybe it is now my time to retire,” he says with a smile.