There comes a point in every new relationship when your girlfriend wants to share a secret. Usually it's to do with sex – how many other partners she's had (with a few conveniently erased) – that sort of thing. Often, the secret changes the basis of the relationship; honesty comes with consequences. But what happens if your new girlfriend has a much darker and more sinister secret than having slept around a bit?

Sitting naked on the edge of the bed in a cheap, sweltering hotel room in the heart of a war-torn, drug-producing region of Colombia, I lit a cigarette and listened as the girl I had just made love with told me a secret dark enough to shake anyone from their postcoital bliss.

I had been in Colombia for a few months to learn how to become a photojournalist. Not by attending some theoretical university course, or taking portraits in a cosy studio, but by pitching myself in at the deep end.

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Times of peace have been rare in the country's history. For the past 40 years or so, a Marxist-inspired rebel group known as the Farc (Revolutionary Armed Forces of Colombia) have been at war with the government, funding their growing army by kidnapping and extortion, and taxing the illegal cocaine trade. Right-wing death squads known as "self-defence forces" have sprung up as a response to the Farc's kidnapping of wealthy landowners and drug-lords. Under the umbrella of an organisation called the AUC (Autodefensas Unidas de Colombia) these private militias, or paramilitaries (known locally as "paras"), are secretly supported by those high in the government and military, who back their dirty war against the Farc rebels.

This triangular conflict has exacted, and continues to exact, a hefty price from the Colombian people. During the past four decades, over 200,000 have lost their lives and more than three million have been forced from their homes by violence or intimidation. This week, following an incursion by government forces to kill Farc rebels in Ecuador, the conflict was at the centre of a diplomatic crisis involving both nations, together with Hugo Chavez's Venezuela.

To dismiss all this brutality as a simple war over drugs does the Colombian people a gross injustice. Its roots are buried in the economic and social imbalance that permeates the country, a huge working class living in poverty, lining the pockets of a tiny, wealthy upper class who own more than 90 per cent of the land, industry and business. My goal, therefore, was to meet and photograph members of each of the groups involved, and to attempt explain Latin America's 40-year conflict.

I began by travelling to a part of the country with a strong Farc presence, and, after much perseverance, persuaded the rebels to let me live in one of their camps. After documenting their daily lives and being alongside them in a firefight against government troops, it was time to go off in search of their sworn enemies, the paras.

I headed towards the Putumayo, one of the narco-trafficking centres and scene of ongoing skirmishes between Farc and the paras in southern Colombia on the border with Ecuador. It took a couple of days travelling on a local bus to get to the capital, Puerto Asis.

En route, I began talking with a fellow passenger, a beautiful Colombian girl called Marylin who told me she was returning from a clothes-buying trip in one of the big cities. I explained my purpose in visiting the region, and Marylin told me she had friends in both the paramilitaries and the military, so would be able to help. She invited me to stay with her family, who had a roadside store and bar on the outskirts of town. I was attracted to Marylin, but had no idea how close we would become and how our future would unfold.

I spent the next few weeks living with her family, making trips out into the countryside to photograph the coca fields and to meet the paramilitaries. Marylin and I spent long afternoons lying together in a hammock. We held hands and kissed occasionally, but it went no further. Eventually, my time and funds ran out and I had to return to England. As I said goodbye, I promised to do my best to return and Marylin told me I was now "part of the family".

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Six months later, I was back, determined to explore this conflict fully, learn as much as I could and maybe publish a book. I made my way back to Puerto Asis with the intention of spending some time with Marylin and her family. But I was in for some surprises: Marylin told me that she had joined the AUC and had been active in combat in the nearby village of El Tigre. Another female friend who had been fighting at her side had been killed, along with 25 other paramilitary fighters and at least 15 rebels. When the combat ceased, the entire population of the village fled. Marylin's brother was now working on a coca plantation and carried a pistol that he slept with under his pillow. I didn't find it particularly shocking. This was, after all, a country torn apart by every type of violence. Only luck, or lack of it, dictated which side you were on.

Months passed. I travelled around the country developing my project. The results received positive attention, including a prize in an international competition, and it was suggested that I go to Iraq to document the war there. And so I did. But, after six months living with the daily car bombings and rocket attacks in Baghdad, I was hankering to return to Colombia.

A year after our first meeting, I arrived back at Marylin's home in a battered taxi. I sat and drank an ice-cold beer with her father while waiting for her to return from an "errand". I then walked hand-in-hand with her and her four-year-old daughter, Natalie, down the rutted cart track to a tree-shaded river behind her house. With her daughter splashing around near the bank we waded, arm in arm, into the deeper, cooler water. I felt there was a change in the atmosphere, but I couldn't exactly put my finger on what I was sensing.

I asked Marylin if things would be different between us if I stayed at a hotel in the town rather than with her family. She agreed that it might make it easier for us to be together, so I found myself a room. That evening, she came for dinner. We ate on the balcony and, as we shared a bottle of wine and listened to the chorus of insects, I began to think that the year of groundwork I had put in was about to pay off. Marylin stayed the night.

Puerto Asis, Marylin's home town sits a degree or two above the equator. Air-conditioning was an expensive extra and I was broke. The tiny hotel room was stifling, and, as we lay curled in the sweat-soaked sheets, with the shouts of street vendors and the rumble of early morning traffic drifting in though the balcony window, Marylin said she had something to tell me.

She then hit me with a confession that would both thrill and confuse me. She explained that in the months that I had been away in Iraq her role within the AUC had changed; she had joined the urban militia and become an assassin. Her job was now to eliminate informers and traitors. So far, she told me, she had killed at least 10 people in the area. I lit a cigarette and inhaled deeply, Marylin looked at me through the smoke as I exhaled, waiting to see how I would respond to what she had just told me.

Strangely, her confession did not have the impact one would expect; I did not recoil in horror. The months I had spent in Colombia and in Iraq surrounded by violence had altered my perspective. I don't think that I had become immune to death or suffering but I had certainly become less easily shocked. The difference between victim and victor, rebel and refugee, often felt like only a matter of perspective.

I had always enjoyed the company of the "doers", the rebels and the soldiers who were out risking their lives for causes I supposed they believed in. I was left cold by the wealthy, well-dressed beauty queens who inhabited the upmarket clubs of Bogota. Although I would later feel very differently, my initial reaction to Marylin's words were an acceptance that may even have bordered on approval. I guess I felt that as war-zone lovers go, she was pretty "cool".

In the beginning, her visits to my hotel room – usually armed with a pistol – did not disturb me greatly. At first, I don't think the real implications of what Marylin was doing had filtered through the surreal haze. I was young and living out a great adventure. This was surely the closest I would ever get to someone who was truly and totally involved and immersed in this conflict. The woman I had only recently begun sleeping with was a hired killer and there was a gun on my bedside table.

Watching her take the pistol from her belt, unbutton her jeans and slip into bed I somehow couldn't quite equate the woman in my arms with the bodies I had seen in the local morgue, their heads shattered by gunshots at close range, murders she confessed to having committed. High on a combination of the heady tropical climate, local rum, grade A cocaine and in the arms of nubile 22-year-old, fantasy and reality became blurred. It felt like I was living in a Quentin Tarantino movie.

One morning, Marylin told me that the previous night she had persuaded a friend to help her decapitate and dismember a woman she had been contracted to kill. This was no informer, but, rather, a friend of hers who paid her to kill her boyfriend's other girlfriend. She described so graphically what had happened, with so little feeling, that at last reality kicked in. I found my feelings about her changing. The romantic light started to fade fast. She no longer seemed to be a legitimate part of a civil conflict but had evolved into a freelance killer, taking life in exchange for money – no more, no less.

Although I still found her sexually attractive and wanted to be with her, something else was ricocheting around in my brain. Some of the thoughts that would have occurred to anyone else much earlier were, now, at last, beginning to filter through.

Over the past year, I had photographed her swimming in the river with her daughter and reading bedtime stories. Now, the images I was recording concentrated almost entirely on the other side of her life. I was, with thoughts of self-preservation in mind, reducing her to "subject".

I asked Marylin if she would be prepared to let me interview her about her life and what she had become involved in. Wearing a balaclava and brandishing a pistol, she permitted me to video our conversation.

I began by asking her how she had first become involved with the paramilitaries and why she decided to join them. How she had been persuaded to kill her first victim and how she felt about it. She started hesitantly, but gathered confidence as her story unfolded.

"When I killed the first person, I was afraid, I was scared. I killed the first person just to see if I could. But there is an obligation to kill. If you don't, they kill you. That's why the first was very hard, because the person I killed was kneeling down begging, crying and saying, 'Don't kill me. I have children.' That's why it was difficult and sad. But if you don't kill that person, someone else from the AUC will kill you. After the killing, you keep trembling. You can't eat or talk to anyone. I was at home, but I kept imagining the person begging not to be killed. I shut myself inside, but with time I forgot everything. The superiors always say, 'Don't worry, that was just the first time. When you kill the second one, it will all be OK.' But you keep trembling.

"The second time is only a bit easier, but as they say here, 'If you can kill one, you can kill many more.'

"You have to lose the fear. Now I am still killing and nothing happens. I feel normal. Before, I had an obligation to kill, I was sent to kill. But once I left the organisation, I was not obligated. I now only do the job for money.

"Yes [I killed one of my friends], because they were going to kill me. They told me to take care because they worked for the other side and had connections with the guerrillas. And so it was my life or theirs. So I asked permission to do it, which [the AUC] gave me. [The AUC] investigated and it came out positive that [my friends] worked for the guerrillas, so I killed them. It was very painful for me. I was at the burial and at the vigil. It hurt me to see his mother crying, knowing I was the one guilty of having caused that. But it's your life and you're taught in the [AUC] school: First you, then the others. In total, I have killed 23 people."

An incredible sadness washed over me as I listened to this intelligent young woman, who I had become so close to, talk of her life. Marylin was an extreme victim of circumstance. Her boredom and quest for excitement had brought her into contact with the paramilitaries, who had brainwashed her and left her with no respect for human life. Not her own, not even her family's.

But her excuses, or lack of them, riled me and I told her she represented everything that was wrong with the country. From my privileged and ultimately unqualified position as an outsider I found it impossible to identify with her, only to be angry, upset and judgemental.

Reducing her to a "subject" had not worked, I did not seem able to be detached and objective or able to put my own feelings aside. I had travelled too far beyond that point. While on one level I relished the intensity of what I was experiencing, there was a price to be paid for getting in so deep and it was high. I realised that the things I had seen and heard in the last couple of months were incredible. Through them, my passion for Colombia had grown and my understanding of what was happening in this much misunderstood country had broadened. But I felt that I had lost something and been damaged by them, too.

I returned to Iraq and then moved on to covering the war in Afghanistan. Over the course of a year, Marylin and I exchanged emails periodically. They mainly involved her asking me where I was and asking me not to forget her. She told me that the things I had said to her after her interview had had a big impact. No one had spoken to her like that, really questioned her about what she was doing with her life. She told me that she did want to make a new beginning, but that she knew the AUC do not let their members leave, at least not alive.

After a long period of silence, I began to fear something had happened. So I decided that I would return to Puerto Asis to learn the truth.

It took me some time to pluck up the courage to drive out to her home to see if she and her family were still around. I wondered if she had perhaps made the break and left to begin a new life or whether, more likely, her past had caught up with her. Given the dreadful things that I already knew she had been involved in, I was at least somewhat prepared for bad news. What I was not ready for was how confusing it was going to be to hear it.

Her family showed their normal surprise at finding me at their front door. All my fears were confirmed as her father, his eyes welling with tears, told me that Marylin was dead. She was 25 years and two months old when she was kidnapped from her home and stoned to death. Her abductors crushed her head with rocks and then shot her.

The next morning, her now six-year-old daughter, Natalie, awoke as an orphan, Marylin's parents had lost a third daughter and her brother so overcome with grief that he was unable to walk, talk, or even feed himself. Marylin was not killed by some local seeking revenge for one of the many deaths that had occurred at her hands during her time as an assassin. She was murdered by her own group in a symbolic stoning for being a sapo ("frog"), which is what Colombians call informers.

Her most recent boyfriend was a government soldier, convenient enough when the paramilitaries and the military were working side-by-side in their war to wrest control of the coca fields of Putumayo from the Farc, but enough to get her killed when that relationship soured and her pillow talk continued.

Marylin's death had a special significance for me, because I, too, had shared some of that pillow talk. We had been friends and then lovers. Our lives never had much in common; except that Colombia's dirty little war had both of us locked into its fatal grip. I found it difficult to speak; I wasn't actually sure what I was feeling.

Was I feeling sorry that a young woman, who had deliberately taken the lives of other human beings, had received the same kind of street-corner justice she had been responsible for handing out? Was I reliving the conversations we had about changing her life and the emails I received from her thanking me and saying she needed to talk more about how she could get out of the mess she was in? Was I wishing I had done more to help her? Was I feeling sorry for her parents and her beautiful daughter, who one day would want an explanation as to why her mother was killed and, maybe, discover the horrors that occurred while she was a sleeping baby? Was I remembering what it was like to kiss her in those days before I had any clue she was an assassin? Was I trying to imagine, or perhaps trying not to imagine, what she looked like after her head had been destroyed with stones and rocks?

In truth, I was thinking, feeling and imagining all of these things. At the same time, though, I knew that whatever pain her family was feeling, she had caused this same pain to others many times over.

Back in my hotel room I let out the longest of breaths, lit a cigarette and stared at the ceiling fan. The whirling blades churned together my memories of the wars I'd been in, my ex-girlfriend and my current situation.

Early next morning, together with Marylin's mother and Natalie, both wearing their best dresses and carrying flowers, I went to see where Marylin body had been laid to rest. Her coffin was in a concrete box, resting on top of the tomb of her sister, who had also been killed by the conflict. The number of bodies demanding burial had long ago outstripped the space available. Alongside lay a much smaller tomb; the remains of another of her sisters, who'd died of natural causes aged three months. I could not imagine how Marylin's mother felt holding the hand of her granddaughter, looking over the graves of all three of her daughters.

My plan for travelling deeper into Putumayo to photograph the paramilitaries no longer seemed such a good idea. Marylin had always pointed me in the right direction and warned me when pushing further was not a good idea. I wanted to learn more about her life and death, but didn't want to get killed for asking the wrong questions of the wrong people.

That night, eating dinner against a background of revving motorbikes and honking trucks, another local told me more of what had happened to Marylin. Between mouthfuls of soup, the woman told me that Marylin had been involved with the AUC a lot longer than she had admitted to me, and that it was commonly believed in the town that she was involved in the massacre of 26 villagers in El Tigre. Many of the victims were decapitated and disembowelled before being thrown into a river. I booked a seat on the next available flight out.

As I watched Puerto Asis disappear below me, the plane was enveloped by cloud. On my iPod, someone was singing "this city's made us crazy and we must get out".

As I sit typing this, nearly 9,000 miles away in a freezing, dark hotel room in Kabul, Afghanistan, covering yet another never-ending conflict, I wonder whether it could have ever ended any differently. Was Marylin really killed because she was an informer or because, as she indicated in her emails, she did really want to leave the AUC and start a new life?

This is what I want to believe. I want to believe that she had a change of heart. I want to believe that she wasn't the cold, heartless, evil killer she appeared to be. But who am I trying to fool?

This article was originally published in Arena magazine. Jason P Howe is the author of Colombia: Between the Lines, out later this year. To order a copy, contact books@conflictpics.com