Jeremy Scahill, whose provocative documentary Dirty Wars is released in the UK this week, has been described as a "progressive journalist" and an activist in the same mould as Glenn Greenwald. Is "progressive" a word he is comfortable with? "It's not a term I would reject in terms of my personal politics," he says, "but I see myself as an independent journalist and my mission is to try to tell stories about real people."

Scahill's critics write him off as an activist or an advocate, but he argues that all journalists have a point of view. "Oftentimes the ones who are activists on behalf of the state don't get labelled as activists. People who accept the state's version of events are considered objective journalists. People who question the state's version of events, particularly in the face of overwhelming evidence that the state is either lying or involved in extra-legal activity, are tarred with the brush of being activists. There is a systematic smearing of anyone who questions the state, while people who are slavishly devoted to advocacy for the state somehow wear the crown of objectivity."

The real people in the film – and the book, Dirty Wars: The World is a Battlefield, which accompanies it – are the victims of what are, in effect, US hit squads operating in Afghanistan, Pakistan, Yemen, Somalia and other places where the American government is waging its "war on terror". Starting with one murderous attack on an Afghan police chief and his family in eastern Afghanistan, Scahill widens the focus to portray an out-of-control US military, operating through a shadowy organisation called the Joint Special Operations Command, stalking an ever increasing number of targets in an apparently endless war. It is a compelling picture that tries to make sense of the spiralling number of drone strikes and targeted assassinations; tries, too, to prise a reaction from viewers who have been desensitised by a decade of such killings.

Reading this on mobile? Click here to view the trailer

Scahill began work on the film in early 2010, when he travelled to Afghanistan with documentary director Richard Rowley, a friend and colleague with whom he had worked in Baghdad. Rowley wanted to make a film about Afghanistan; Scahill wanted to examine President Obama's hawkish foreign policy. They have ended up doing both. "We started to investigate a series of night raids [by US forces]," says Scahill, "and discovered that the people doing the raids were members of this elite secret unit. When we realised where else in the world they were operating, we realised we had a film."

Members of a western-backed Somali militia in Mogadishu in a still from Dirty Wars

Scahill co-produced, co-wrote and narrates Dirty Wars, the noirish style of which is reminiscent of the Oscar-winning thriller Argo; the dark, cropped-haired Scahill even bears a resemblance to Ben Affleck. Most documentaries prefer an unseen, omniscient narrator, and some critics did not take kindly to the journalist's very visible role when the film was released in the US in June. "Scahill's so busy Being A Reporter – capital letters are definitely called for – it gets in the way of what he's reporting on," complained Mark Feeney in the Boston Globe. "[He] comes across as a maddening blend of nobility and narcissism."

Framing the film in terms of the reporter's own journey was clearly a crucial decision. How tough was it to make? "Excruciating," admits Scahill. "I resisted it fiercely for months. Rick [Rowley] wanted to make a film that was about me doing an investigation, and I wanted to make a film about an investigation. We agreed on something in between early on, where I would be on camera but I wouldn't be myself. I would be like a tour guide through the archipelago of these global wars. Rick was always wanting me to have personal reflections, but I was resisting."

What emerged from that compromise after a couple of years' filming was a four-hour rough cut that failed on all counts, threatening to bury the audience in facts. "It felt completely fake," says Scahill. "It had no soul, no story, and because I wasn't myself, it just seemed like I was acting. I was pretending I don't actually care or that I don't have emotions about these things." They brought in a co-writer, David Riker, who encouraged Scahill to turn it into a more personalised journey, which he does with the sort of narrative that could come from a Raymond Chandler movie.

He accepts that placing himself centre stage will attract flak, but it's not Feeney's accusation of narcissism that bothers him. It's that western audiences will only watch a film about wars in Muslim countries when a fellow westerner is in the lead role. "I was on a panel in Washington DC with a young Yemeni activist, and she asked why it was that white men always had to make sense of these stories for the world in order for anyone to pay attention to them. I agree with that critique, and I don't feel completely comfortable with my role in this film. I tried to tell it in a different way, but it wasn't working, so even though it's a flawed vehicle and it's hard for me to even watch the film I think we made the right decision."

Jeremy Scahill in Somalia, in a still from Dirty Wars

What he doesn't apologise for is the fact that it looks like Argo. "We made no secret of the fact that part of our inspiration for the aesthetic of the film comes from the style of thrillers. Because I felt so uncomfortable with being on camera, we would make a joke that I was just a stand-in and Matt Damon would be arriving on the set at any moment." The serious point is that it allowed them to make a documentary that could reach a wide audience. "We didn't want to make a film that was preachy or holier-than-thou. We didn't want to take people along with an all-knowing expert, but to experience what it was like for a journalist as they discover more pieces of the puzzle they're trying to assemble."

Scahill, who is 39, volunteers some biographical material to underline his argument. "I'm from the mid-west of the United States, from Wisconsin," he says. "Both of my parents are nurses. My entire family are working-class people. I wanted to make a film that my uncle, who's a construction contractor and never pays attention to these issues at all, would be able to watch, absorb and feel like he walked away understanding something about this extraordinary moment that we're in in this post 9/11 world."

On those terms, Dirty Wars succeeds. The extent of the US military's covert operations and the amount of "collateral damage" are shocking; the film shows that even US citizens have been the victims of non-judicial executions; and the argument that the war on terror is ultimately unwinnable because indiscriminate killings radicalise whole populations is persuasive. "Somehow, in front of our eyes, undeclared wars have been launched in countries across the globe; foreigners and citizens alike assassinated by presidential decree; the war on terror transformed into a self-fulfilling prophecy," Scahill laments at the end of the film. "How does a war like this ever end, and what happens to us when we realise what was hidden in plain sight?"

The ruins of Mogadishu cathedral in Dirty Wars

Scahill's activism started early. He dropped out of college without taking his degree – he was studying history at the University of Wisconsin – and spent a year working at a homeless shelter in Washington DC, cleaning toilets, mopping floors and taking elderly men to doctors' appointments. He started listening to the leftwing news programme Democracy Now!, which had just been launched on the Pacifica Radio network. "It was the most incredible thing I'd ever heard," he recalls, "and I basically began stalking its presenter, Amy Goodman, and sending her letters saying 'I want to do what you do. I'll walk your dog, I'll look after your cat, I'll make you coffee.' Eventually she had to decide whether to get a restraining order against me or let me come and volunteer for her. So she let me volunteer, and I learned journalism as a trade by working with Amy Goodman."

In the late 1990s he worked on TV shows with radical film-maker Michael Moore, whom he calls a "master communicator", before moving on to the Nation magazine, where he became national security correspondent, reporting on a succession of wars and writing the bestselling Blackwater: The Rise of the World's Most Powerful Mercenary Army. In the film we see Scahill struggling to come to terms with ordinary – too ordinary, as he finds it – life back home in Brooklyn. "I've done this kind of work [reporting on wars] for my entire adult life," he tells me, "and I realised in the course of making this film that it changes you as a person. You come back from a war into your own society, and you feel like you can't relate to anyone. But also you carry around with you the stories of all these people who have let you into their lives and shared with you the excruciating pain they've experienced. That is a huge responsibility we as journalists carry. Sometimes we try to tell ourselves 'Oh, I can steel myself. I'm not going to let it affect me. I'll move on to the next conflict.' I saw people like that, and I don't ever want to be that person."

But isn't it tough to carry the scars of all these conflicts – the family in mourning in Afghanistan, the morgue full of children's corpses in Yemen, the gun-toting anarchy in Somalia? "Yeah, it is," he says. "We would go into people's homes and I would promise we were going to bring this story back and tell it in America. We didn't know if we would be able to do that, but we were promising them that. There were images of children I fought to keep in the film because I remembered sitting with family members and saying 'They're going to show this film.' I take that responsibility very seriously."

Scahill in Yemen, from Dirty Wars

He says the need to tell their stories outweighs any fear he feels that he might himself become collateral damage while reporting, or the paranoia that afflicts anyone who stands up to the state. In the film he mentions being harassed by anonymous phone callers and believing his computer had been hacked. He says that, as the Edward Snowden furore shows, journalists are under greater pressure than ever before. "Under President Obama the US justice department has authorised the seizure of the phone records of journalists; they are tracking the meta-data of journalists; they're prosecuting whistleblowers in record numbers under the Espionage Act; there really is a war against journalism. For everyone who does this kind of work, where you're taking on powerful institutions, the responsible posture to take is to assume they're monitoring your communications. It's a part of doing this work."

Is it possible to have a life beyond the war zone? "You can," he says, "but it takes special kind of person to agree to be in a relationship with a war reporter. The battlefields of the global wars are filled with broken marriages. I remember during the really intense period of the Iraq war in 2004-5, the circle of journalists that I was around were all just broken, shattered people enduring the hell of that war. A lot of people were drinking themselves into oblivion. Journalists have post-traumatic stress disorder just like soldiers do. Some try to deny they have it and believe they can float from assignment to assignment, but it always catches up with you."

There are also the conflict junkies who need the drug of the battlefield. "I'm not that kind of person," says Scahill. "I value human life and don't get pleasure from being around men with guns or hearing things explode. I'm motivated more by wanting to tell the stories of people who are on the other side of the missiles." Having finished Dirty Wars, he has no desire to rush back to the battlefield. "I don't want to do this again any time soon. I feel gutted as a person. I've been living all these stories and talking about them every day for the past four years. I've internalised a lot of it, and it consumes my thoughts. I can't ever imagine I'll be anything other than a journalist, but it definitely took a toll on me. I don't know what I'm going to do next journalistically, but I do know that I need to regain my footing in the world."

• Dirty Wars is released in the UK on 29 November