This month marks the 20th anniversary of the worst massacre in Europe since the second world war. It’s estimated that more than 8,000 Bosniaks (Bosnian Muslims) were rounded up by soldiers from the Republika Srpska and killed in and around the town of Srebrenica. Deemed an act of genocide, it was a war crime that came to symbolise the ugliness of the ethnic disputes that set the Balkans aflame in the 1990s.

But amid the fighting and chaos that followed the break-up of Yugoslavia there were other sorts of war crimes that, while not as murderous, represented a particularly humiliating and psychologically damaging form of violence. Somewhere between 20,000 and 30,000 Bosnian women are thought to have been victims of militarised or systematic rape during the three-year conflict.

“Women were often deliberately kept in detention until it was too late to get an abortion,” says Belma Becirbasic, an award-winning writer and activist in the area. “Some of those who gave birth to babies murdered them and many abandoned them immediately after. Women were reluctant to speak out about the suffering they’d endured. Most still remain silent due to the fear that the perpetrators would not be punished, but mostly out of the shame of being shunned in a highly patriarchal society.”

Although abuses took place on all sides, the bulk of rapes in Bosnia were perpetrated by Bosnian Serb armies and militias and the large majority of the victims were Muslim women. How many children were born as a result is again a statistic that is unknown. “Rumours have been extraordinary,” says Becirbasic, “going from several hundred to several hundreds of thousands.”

She warns that exaggeration of victims on both sides has been a central tactic in maintaining ethno-nationalist hostilities. As Charli Carpenter writes in her book, Forgetting Children Born of War, rape-related pregnancies became a “staple trope in media accounts of the war”, with reporters competing to find newsworthy female victims. But that doesn’t mean that there weren’t plenty of cases of children born from violent conception.

One such child was Alen Muhic. He was born in Gorazde hospital in 1993. “When I heard him cry,” his distraught mother later said, “I asked the doctor to bring him to me. I wanted to strangle him.” But she didn’t kill her son. Rather, she abandoned him in the hospital and walked out of his life, apparently forever. The hospital workers took pity on the child and one of them, Muharem Muhic, the hospital caretaker, who had a wife and two daughters of his own to look after, decided to adopt the baby boy.

For the first 10 years of his life, Muhic lived in happy obscurity, ignorant of the details of his conception and the identity of his real parents. Instead, he believed he was the son of Muharem and his wife, Advija, and brother to their daughters. Then one day in 2003, the story goes, Muhic got involved in a playground fight and his angry opponent told him that he was a “Chetnik bastard” – Chetnik is a derogatory term for a Serb, a reference to the nationalist Serbian militia active during the second world war – and that he was adopted.

Around the same time as this incident Muhic met a film director named Semsudin Gegic who happened to know his biological mother. According to the director, the meeting was a coincidence: he was filming on the land of Muhic’s adoptive parents and the boy independently approached him to make a film about his life. The film Gegic made, in 2004, was called A Boy From a War Movie.

It was a short film, a strange synthesis of documentary, re-enactment and impressionistic flights of fancy. But it was a breakthrough moment. Previously, there had been little or no open discussion of this shameful episode in Balkan history. Now here was a 10-year-old boy, led by Gegic, telling his strange, benighted and touching life story.

The film made a big impact at the Sarajevo film festival, was shown in Moscow and won an award at the Sofia film festival. It also paved the way for Grbavica, a feature film by Jasmila Zbanic that came out a couple of years after Gegic’s short film and won the Golden Bear award at the Berlin film festival in 2006. Although Grbavica also deals with the fallout of the campaign of systematic rapes by Serb forces, it focuses on a single mother in Sarajevo and therefore deals with the subject from a more overtly female perspective. Nonetheless Gegic has a point when he says he initiated the artistic debate about this particular aspect of the war.

Jasmila Zbanic’s Grbavica won a Golden Bear award at the Berlin film festival.

But if A Boy From a War Movie shed light on a neglected corner of the Balkans’ recent past, it also raised more questions than it answered. Who were Muhic’s biological parents? Unbeknown to the audience, the mother did appear briefly in the film as an unnamed and disguised victim of rape. But there was no mention of her biological relationship with Muhic.

What became of her and the rapist father? And what was going to happen to the young boy with the heavy weight of his criminal creation to bear through his tender years.

A decade later, Gegic returned to the story and the result is a full-length film that once again mixes elements of documentary, drama and what Gegic calls his “artistic vision”.

I meet the director at a screening room in a cinema in central Sarajevo. It’s a small, beautiful city, surrounded by dramatic hills on which once stood lethal Serb artillery positions. For almost four years during the 1990s, the town was effectively cut off and subject to relentless attacks. It is said to be the longest siege of a capital city in modern warfare. Almost 14,000 people were killed and more than 5,000 of those were civilians. Although there has been a great deal of rebuilding and regeneration, there are still many battle-scarred buildings that testify to the brutal conditions the inhabitants of Sarajevo endured.

Just across from the cinema is a memorial to children killed in the siege. Almost every aspect of Sarajevo’s rich and troubled history is cheek by jowl. It’s what lends the place its distinctive atmosphere of close-knit cosmopolitanism. Famously multi-ethnic, it has long paid host to three main communities: Muslim, Orthodox Serb and Catholic Croat.

Sarajevans are proud of the manner in which an Ottoman mosque will sit next to a neo-classical church and how, up until the war, nobody much cared or noticed which faith, if any, their neighbours followed. The other aspect of Sarajevo’s compact size and eventful history is that you can walk in a few minutes from the spot at the Latin bridge where Archduke Ferdinand was assassinated, thus sparking the first world war, to the Markale marketplace, whose lethal bombing by the army of the Republika Srpska led to Nato’s intervention in 1995 and the eventual cessation of the war.

Gegic is a sprightly, bearded character in his mid-60s who, by way of introduction, lists his achievements as if he were proffering an extended CV. He tells me how representatives of Vanessa Redgrave and, separately, Martin Scorsese and Robert De Niro sought rights to screen A Boy From a War Movie. He runs through his various awards and informs me that the applause “lasted for 13 and a half minutes” after its screening at the Sofia film festival. It’s fair to say that the director is not the kind of man who keeps an eye out for a bushel under which to hide his light.

After he made the film, he withdrew it from circulation in Bosnia because some critics suggested that he had exploited the young Muhic’s need and vulnerability. “For several years after that I did not feel safe about my own life or that of my family in this country,” claims Gegic.

From whom did he feel under threat?

“Everyone and everything,” he says, perhaps a little melodramatically. “Because I did really put the lives of my family in danger by helping Alen come forward with his identity and his story. There were discussions in the media about alleged abuse by me of this child for whatever purposes. There were telephone threats. People would stop me and call me names in the street.”

He says that his reputation was saved by the work of American researchers, specifically Charli Carpenter, who showed that “I was the one who helped Alen Muhic to step forward and say, ‘I am not an invisible child any longer. I am visible now.’”

Becirbasic agrees. “It seems to me this long-lasting collaboration with Gegic has helped Muhic reconstruct his tragic and complex background or, to quote his own words, ‘liberate his identity’. He should know.”

Muhic became something of a local celebrity. Interviewed repeatedly on TV and courted by politicians, he was turned into the poster boy for a sort of Bosnian stoicism in the face of relentless provocation. In a country that felt itself to have suffered a form of national rape, Muhic symbolised an indomitable spirit of survival.

In any case, after finishing the original film, Gegic says, he told Alen to stay in touch and that if he ever needed anything to get in contact.

“He called me a year and a half ago. He said, ‘I have a suspicion that you are the only person who knows both my biological mother and my biological father. And I want you to help me find them.’”

Gegic says he didn’t give Muhic, now a strapping young man, a straight answer, although he agreed to help him if they could make another film together.

Interview with Alen Muhic

“I didn’t tell him the truth that after this first short film was screened, his mother called me from the United States and she kept calling. One night, she would call me and ask me to film her as well, and the next day she would call and threaten that she would kill me, poison me.”

Another consequence of the first film was that Muhic’s biological father was finally forced to undergo a DNA test and when it was proved that he was indeed the father, he was tried and convicted of repeated and violently aggravated rape. He was sentenced to five and a half years in prison.

But after 18 months, two protected witnesses from Foca, where the crime had taken place, came forward to claim that the biological father and mother were in a relationship before the war.

“That really has nothing to do with the rape he was sentenced for,” Gegic rightly points out. The father also suggested that he wanted to get to know his son. Taking this information into account, the judge reduced the rapist’s sentence to 18 months and he was immediately released.

The situation, then, was complex, contested and fraught with difficulties. In other words, the ideal scenario for a searching documentary. But that’s not exactly what Gegic made. I watched the film, called An Invisible Child’s Trap, with him in the screening room. There were no subtitles so a translator gave simultaneous English translation in my ear.

The first thing to notice is that there are two people “playing” Alen: Muhic himself and an actor who performs as a sidekick and alter ego. Why two Alens?

“Alen is a child with two identities,” Gegic tells me after the screening. “All children like Alen have two identities. He was truly afraid of the emotions he might express if he met his biological parents, especially his father. And being a director I was also afraid of that. So this is why I introduced this second Alen as a sort of defensive mechanism.”

This was not documentary film-making in the Anglo-American tradition. At times, the “acting” seemed amateurish and at others the real-life scenes appeared a little too professionally arranged. But perhaps the most surprising detail in a film about Muhic’s search for his biological parents is that neither of them appears at any time, with the exception of a brief piece of news footage from the father’s trial.

The advance word on the film, as put about by Gegic, strongly suggested a resolution, revelatory or cathartic, and there was more than a hint in our arrangements that I would be able to speak to the biological mother. Yet she was more absent from the second feature-length film than she had been from the original short film.

However, Gegic told me, Alen did meet his biological father, so why wasn’t this scene included in the film?

“My initial intention was to close this film with the meeting between him and his father,” says Gegic. “But as far as his father goes, he’s going to be part of the third film. This is meant to be a trilogy. I’m working on the third part. It already has a name: The Shadow of White Donkeys.”

Perhaps sensing how perplexed I was that a documentary about a son’s search for his rapist father omits the moment when they meet, not to mention the bemusing relevance or otherwise of white donkeys, Gegic added: “If I made it a part of this film, which I could still do, then it would create a problem, because Muhic wants to seek a retrial of his father.”

Alen Muhic, photographed in Sarajevo in June. Photograph: Edin Tuzlak/The Observer New Review

The following day, I met Muhic, who travelled in from Gorazde, where he works as an orderly in the hospital in which he was born. He is a quietly spoken, rather shy young man of 22, with a body-builder’s frame and a busy cigarette habit.

We sat with Gegic in a cafe above the cinema. In the same way that it’s impossible to distinguish Catholics from Protestants in Belfast purely from their appearance, it’s mostly the same in Sarajevo as regards the Muslim, Catholic and Orthodox communities. There are no ethnic differences to speak of. Although some Muslims have taken to wearing beards and headscarves since the war, the large majority still look and behave (drinking alcohol, eating pork) no differently to Serb and Croat Sarajevans.

All that really testifies to religious background are names. When Muhic was a boy, he was nicknamed Pero – a common Serb name – by others in his neighbourhood in Gorazde. He didn’t like the questionable provenance that the name suggested. Was he concerned about his identity now?

“I declare myself as a Bosniak and a Muslim because this is the environment I grew up in and this is what my family declares themselves as,” he replies between drags on his cigarette. “But, you know, I don’t really have this strong religious or national identity. If I was born in any other group, I would just declare myself as part of that. I have nothing against any religion. In essence, they are all the same.”

It’s a noble response, although a familiar enough one in many parts of Bosnia, even today. But Muhic’s whole life, from his very conception, has been shaped and determined by these ancient group identities and recently cultivated animosities. They were almost certainly a key part of the motivation and self-justification that led his father to rape his mother.

Alen Muhic with film director Semsudin Gegic at a screening of An Invisible Child’s Trap. Photograph: Edin Tuzlak/The Observer New Review

That can’t have been easy knowledge for Muhic to absorb and it must have grown much more difficult when he finally encountered his biological father. In the film, we see that, through an intermediary, Muhic’s father makes it clear that he doesn’t want to meet his son. In response, Muhic says, he decided to abandon his search.

Then one day a Muslim cleric from a neighbouring village to Muhic’s biological father called the young man and tipped him off about his father’s presence.

“So I thought about it quickly,” says Muhic, “and then I told my friend, ‘Since he’s here, let’s try to meet him.’”

He was very nervous as he approached the house in which his biological father lived, uncertain of what sort of welcome lay in store. The now middle-aged man came to the door and told Muhic that he knew who he was because he’d been following his story and also looking at his Facebook page.

“So we started talking,” says Muhic, stubbing out one cigarette and then lighting another, “and then we came to the topic of whether he was my father or not.”

The palpable tension as Muhic describes the conversation only confirms that it would have made a dramatic climax to the film, had it been filmed and included.

“First of all, he spoke only about the war, then as we moved to the topic of my paternity, his voice became agitated and he said that he was not my father, that he had never committed any war crimes and that he had been framed, set up.”

They spoke for about an hour. Muhic says that the family living next door to his biological father had told him that he reminded them of the older man so much that it was like talking to him when he was a young man. “And I realised when I was talking to him that it was as if I was looking at myself 20 years from now.”

Yet at the same time he experienced no personal affinity or filial feelings of any kind for the older lookalike in front of him. By the end of their conversation, in which his biological father flagrantly denied being his father, in spite of their resemblance, the DNA evidence and the court verdict, Muhic concluded that he never wanted to see this man again.

“He is trying to make himself a victim, as if bad things were done to him, when he actually committed crimes. He is my biological father on paper, but that’s all he is. I would not even call him a person. For what he’s done I would call him a monster.”

As for his mother, he says his feelings towards her are the very opposite of those he harbours for his father. “I would like to meet her and I don’t blame her for anything. I don’t even blame her for leaving me or not getting in contact with me for the last 20-odd years, because of what happened to her.”

He now has her phone number and, he says, he’s tried calling several times, but either she didn’t answer or the connection was too bad to speak. “One time her husband answered but I didn’t feel like talking to him. One of the main reasons that I would like to meet her is that I learned that she has two sons in this marriage and I would like to meet my brothers or half‑brothers.”

Gegic says she had twice said she was coming to Bosnia, only to pull out each time. But the plan was that she would come this month. Again it’s Gegic’s intention to put this reunion in a third film.

Muhic’s extraordinary story is one that represents a whole range of dark conflicts – not just those that ravaged the Balkans, but also those that exist between truth and falsehood, between rapacious males and their female victims, and our own internal conflicts that forge our complex identities. Yet for all its emotive richness, it’s not a story that requires a third film.

Instead, Gegic should take all the footage he’s assembled over many years and fashion one single and compelling document about Alen Muhic. It could show how an abandoned baby boy in a war-torn corner of Europe went in search of the real story about his parents and found out a vital truth about not just himself but also the human condition. Where we come from will always matter, but in the end, after all the pain and humiliation and setbacks, not nearly as much as where we’re going.