A man steps across the floor of what seems to be a basement or dungeon, on a film shot by a wobbly, handheld camera. Blood, sticky underfoot, runs beneath his boots – and the camera catches what seems to be a severed head. The scene is being played on a computer screen, watched by an intense young man, transfixed. A beautiful girl looks also, over his shoulder. "Is that Iraq?", she asks, squirming at the degenerate and apparently gratuitous cruelty. "Mexico," replies the man with a grunt, clearly terrified himself. Welcome to the latest film by Hollywood's – even America's – heretic-in-chief, Oliver Stone. Unsurprisingly, this brief exchange is charged with greater meaning than it appears at first sight, and the film's director has come to elaborate.

The physical presence of Oliver Stone is not unlike that of his impact on cinema over the last four decades. He is immediately contrapuntal: tanned leathery skin, khaki waistcoat and black boots in the seamless, breezy tranquillity of a grandiose hotel in Berlin, answering waiters' questions in polite German with a growl, complimenting the pretty-prim waitress on her looks with a gravelly chuckle. And when he gets down to the business of explaining his new film – sleeves rolled up, hair like that of an old rocker (which he is) – there is no polite prologue to the heresy. "Yeah, this is one of America's wild wars that never ends and ain't going anywhere: the war on drugs." After all, this is the man who has – famously or infamously, depending on who you are – subverted and scorned every norm, rhyme and reason on which the narrative of the US political establishment (and America's strut in the world) is premised, his canon thereby so much greater than the sum of its parts.

Platoon and Born on the Fourth of July were pivotal contributions to America's attempt at reckoning with its own self-generated catastrophe in Vietnam; JFK, Nixon and W. retold and revolutionised received wisdom on the death of one president and the lives of two others. World Trade Center rescued the human story of 9/11 from that manipulated by Washington for its own reasons.

Perhaps most cogently of all, with hindsight, Salvador, from 1986, was among very few films or mainstream expressions of any kind which looked at the dirty war that ravaged the Americas during the 1980s through a Latin American lens, repositioning President Reagan's role as more that of jackboot than sponsor of the freedom he claimed to be spreading, through alliances with dictators and death squads. And more recently, South of the Border stood and stands as the only attempt of its kind to document a new dynamic across the hemisphere, and the rise of newly confident leftwing leaders in the Latin Americas, unbowed by the colossus, the US. Stone's latest, Savages, is to be seen in that vein – only the story concerns the country that is a mere 20 minutes walk from Texas across the Rio Grande, and just south of the border from the golden beaches of San Diego. It addresses the first war of the 21st century (which gives us a glimpse of what the rest of it may well look like), the narco cartel war in Mexico.

Of course Stone is drawn to this: Mexico's war – if that is what it is – has claimed 50,000 lives, and has done so with striking and baffling cruelty. "A lot of these people have died slowly," says Stone, approaching his theme. "I didn't want to show people being dissolved in acid, and there are plenty of other things we could have shown but didn't, or had to cut."

Indeed there are: in his hypothetical but meticulously researched film Stone does not detail the sewing of a flayed face to a soccer ball, or the decapitated bodies left dangling from bridges, mutilated corpses strewn along highways or filling mass graves. Strangely, though, the US media seems as keen to avoid mention of the daily litany of death across its underbelly as it is to cover it; even less does the American establishment want to understand why all this is happening, and consider the possibility that there may be deep-rooted economic causes of at least aspects of Mexico's agony for which the US bears some responsibility, quite apart from its insatiable need to consume drugs and welcome the profits they generate through its banks.

High time for a major film about all this, in an America which, as Stone says, "doesn't give a shit" – even though the violence is next door and spilling over the US government's fence through the desert, in defiance of Washington's militarisation of the sieve-like border. America wants there to be a wall along the 2,000 miles it shares with Mexico, like the one that once ran beneath the window at which Stone sits in Berlin. But that is not going to happen when the border is also the busiest commercial frontier in the world, crossed by a million people every day.

At first sight, Stone may seem to have flinched from making this badly needed film. Savages is not for the most part set in Mexico, not is it overtly about Mexico, as it might have been. It is an adaptation of a novel by the great American writer on the border and drug war, Don Winslow, about two men: Chon, a traumatised veteran of Afghanistan and Iraq, and Ben, a karmic botanist par excellence. Their combined experience and knowledge enables them to grow marijuana of unrivalled potency and quality. It also helps them secure the devotion of lovely blonde O, whom they share as a narcotic-erotic ménage à trois.

Stone's generic Baja cartel, led by a matriarch called Elena, is set on acquiring the seed if not its growers, and kidnaps O in pursuit of this aim. The boys react heroically, and set out to rescue their woman. In the background is an aspirant deus ex machina, Dennis, a corrupt agent for the Drug Enforcement Administration, who works alongside not only Don and Chon, but also the cartel's vicious enforcer on the US side, Lado.

There is detail in the film which Stone is the first – and only one, north of the border – to grasp, and the detail is important in reading not only this narco war, but also what it means to modern capitalist society. First is the perverse innovation in the cruelty, for its own sake and its recreational aspect. Stone treats us to the execution of a suspected snitch, hung by his wrists and whipped until he confesses (even though he is innocent), after which he is incinerated alive with a tyre around his arms and torso, running in wild circles to his death. During the scene, there's a moment of mastery: the soundtrack, the cackling laughter of those watching. It takes Stone to work that out. Yes, in Mexico's war, this is fun. "It's getting crueller out there," muses Stone. "It's gone up a level."

Another insight is the cartels' mastery of the internet and along with it their satanic sense of humour. The tit-for-tat over kidnapped O is conducted largely through cyberspace, and at one point the cartel sends our heroic duo an animated cartoon of the decapitation of their girl. And there is this about the real-life cartels: unlike the Bosnian Serbs or even al-Qaida, they do not need to speak to us, to the media or politicians, except on their terms. They control their message, they do so through their own mantas or banners, sick but funny notes pinned to the more illustrious victims' mutilated corpses, but above all through the internet – and in doing so they laugh at us. They have no cause to proselytise, nor is there any retort to them – that is their sick genius, and that is why they laugh. "Yeah – that humour thing," says Stone. "It's something else. It takes someone who knows what's going on to understand it, the humour and the cruelty. I was scared of it, but I wanted to make sure I could keep time with what is going on."

One of Stone's hallmarks, in films such as JFK and W., is that he make you suspend disbelief so thoroughly that you can be forgiven for thinking you're observing the real thing, not a dramatisation. In Savages Stone has mercilessly captured the horrific details of Mexico's war and it is tempting to ask why he opted for an action movie with rather annoyingly gym-cut Colgate Californians and a Barbie-blonde stoner as its central characters, instead of something that gets us inside Mexico. Inside, if not the Tijuana cartel, which is now, as Stone himself admits, "dealing with small pocket change", then a film about those others who are redefining what a narco cartel – indeed, criminality – is in the new world and global economy. The paramilitary Zetas, for example, are an entirely new breed of syndicate, utterly ruthless, apparently unstoppable. It seems a shame that even a film by America's most irreverent director (who has looked at the US through a rare Latin American eyepiece) must be centred on the United States. One would like Stone's take on the world's most wanted criminal, Joaquín "Chapo" Guzmán, fugitive leader of the Sinaloa cartel, or his nemesis, who has overtaken even him for savagery, Osiel Cárdenas Guillén, founder of Los Zetas.

But actually I am missing the point completely, thinking this way. Stone has a terrifying and convincing thesis as to why the film has to be set in America, with American characters: "The point," he says, "is that wars come home, they come home to roost. And there are connections: one of the two main guys has come home from Afghanistan and Iraq, and he's brought all that with him, what I think are new levels of cruelty and combat technology we have out there."

He drives his theme: "Of course, humankind has always been cruel – the Third Reich and so on. But I think there are new levels of cruelty, new technologies now, a new ball game. Maybe I'm wrong, but the cruelty level in the world just went up in these recent wars. We get a lot of information about what's happening in Iraq, the Middle East and Afghanistan, which comes back to America with this guy. And who knows how this may influence what's happening in Mexico – I think it probably does."

It's a shocking but cogent point about the nature of the violence, and its arrival into our public domain. Stone cut his teeth in Vietnam, where images of violence (the famous girl on the bridge burned by napalm; and scenes from Stone's own films and past as a veteran) were supposed to shock us – and did. Now, in reality, all that has volte-faced: the Zetas relay their own atrocities on the web as recruiting posters, and in Stone's film, to parley with their proposed business partners. It has been posited before that the Zetas got their ideas for torture and execution videos from al-Qaida, who in turn respond to souvenir photos taken by American troops of their own abuses in Abu Ghraib. Stone, typically, hurls us to the logical, heretical, conclusion.

"This Middle East thing brought it to another level. The barbarism came back in a big way, and it was Bush who started that. It all began with Afghanistan and Iraq. The guy in the movie brings it home; and the cartel brings it home."

There are cinematic considerations too: "It's based on Winslow," says Stone, "and we've made it into a thriller. No, I don't think the cartels would work that way with independent marijuana growers in California. No, there aren't any IEDs going off in the Californian desert – but," and he grins with inimitably Stoneian mischief, "I like the idea!"

Another subtlety is Stone's depiction of the fall of Elena, the matriarch. This occurs as the result of a mutiny by Lado, who has switched sides to a rival, El Azul, and because she comes to California to visit her daughter. Her collapse – and with it, by implication, that of her cartel – could signify the arrival of a greater power, a new cartel led by El Azul. This has happened in real life: Guzmán has defeated the Tijuana cartel, which was led by one of the first female capos, Enedina Arellano Félix. It could be because "it's tough taking orders from a woman", observes Stone of Lado. But it could also be seen as Elena's weakness of character, or at least her old-fashioned view of what a cartel's code should be. As Stone puts it: "She's a good traditional woman. She's proud of the fact that her daughter is ashamed of her. And her fall is the fall of the don. Elena was weak because she had a thing for her daughter and wanted to rescue her." This is exactly it: the mutation of Mexico's cartels from the don of old, with his (or her) attachment to family and codes of honour, however criminal or perverse they were, and the transfer of power to those whose only code is raw ruthlessness – like Guzmán or, to an even greater degree, the Zetas.

In Savages, the DEA agent Dennis is corrupt and credible. He protects Chon and Ben for money, takes a bribe to deliver them Elena's daughter, and gets to strut and moralise at a press conference when Elena is finally felled – having himself switched allegiances to El Azul along with his contact, Lado. The role is in part shaped by a former DEA agent Stone hired called Eddie, who had "30 years experience. He was in the Middle East and he knew the scene in Mexico. I got into the DEA that way – Eddie took care of us; and getting that kind of insight into the DEA is a big deal."

Lado is a credible character who "wants to be an American", says Stone. "He takes his kids to little league, his wife worries that he's out last thing at night with his 'gardening business' – his cover, and of course he has other women. He comes in one night, and she can smell a woman on him and he takes her apart, he rapes her – but we had to let that scene go."

Lado "also has eight or nine chihuahuas at his feet", observes Stone, and it is a detail to relish though the scene was cut: "I've been to a couple of these drug lords' places", he says, "and it's like ocelots to them. They've got all these hairless chihuahuas, proud of the fact that 'they cost me a fucking fortune'."

Stone's conclusion focuses less on the economic backdrop in Mexico than the failure of the war on drugs. Stone of course takes this further, entwining his themes. First: "That border is going all day and all night long. And it's 2,000 miles long. There's no way they're going to stop this. Dammit – they tried to build a wall across Berlin!" He gestures out of the window towards Starbucks, where no-man's land used to be: "Walls don't work, period." And second: "I don't see anything coming out of this so far as the war on drugs is concerned. It's been 40 years now, and its just become a method by which more money can be generated to fight what they now call narco-terror." And here's the crux, the entwinement again: "Drugs and terror, they couple them together, and the drug war becomes part of the war on terror that never ends. Part of the total terror that is overcoming our lives."

Apart from connections to the Middle East already made, it is impossible to continue in this vein without invoking South of the Border – indeed it is impossible to discuss any Stone film in isolation from the others.

South of the Border is a documentary series of interviews with those who are bringing Latin America to a new critical mass, a shift in power vis-a-vis the United States. All of them are elected, leftwing presidents of countries that have been, as Stone puts it, "in Uncle Sam's backyard", but which now brandish a new self-confidence, after decades of American puppet regimes: Néstor and Cristina Kirchner of Argentina, Luiz Inácio da Silva of Brazil, Rafael Correa of Ecuador, Evo Morales of Bolivia, Panama's Fernando Lugo and, famously, Hugo Chávez of Venezuela.

In January 2008, Stone's audacious recent history on the theme ofSouth of the Border began in this newspaper, with an interview he gavethe Observer in Bogotá in which Stone refused to condemn the Farc guerrillas, with whom he was trying to negotiate the release of three hostages. With him were Néstor Kirchner and Hugo Chávez. "I remember it well!" he half-laughs now. "I was on a mission. I wanted to stay low key. Néstor was there, and Hugo, and the American Red Cross, flying into this shithole of a town. Anyway, the Red Cross helicopter arrives, and, well, it was called off. The Farc people are always wary of the CIA, and I think the Americans just couldn't have Hugo involved in anything that would be a success – the hostages were released shortly afterwards, after Hugo had gone."

He reflects now on the wider theme: "The numbers don't lie. These are countries which have seen growth and real improvements after being failed by neo-liberal economics. The US took the side of the bad guys constantly – the media covering up so many of the abuses, in Argentina, Chile … But now, for the first time, these countries have thrown off the stranglehold of the International Monetary Fund and US treasury, which made loans the terms of which were those of what they call the 'neo-liberal Washington consensus' – [to] not only pay back the loans, but conform their economies to the privatisation of the kind we have here: hospitals, military, prisons. Well, in South America, privatisation did not work, it had disastrous consequences.

"And what they essentially did in the last 10 years was to throw off that tyranny. Their people have suffered so much, and they voted in new leaders. But even after they were elected, these people were resented by the US. I've never read one positive word about anything these people have done in the US media – let's face it, the Americans don't accept the idea of the election of leftwing leaders in their own backyard."

Accordingly: "Each one of these leaders has been picked off, one by one, by the United States … Disunite them, break them off from each other. But they've stood firm, and I think this is an important moment. They've done good for their countries, and I hope they last."

There is a connection between Savages and another Stone film, in fact two of them: Wall Street and its recent sequel, Wall Street: Money Never Sleeps. Chon and Ben have a money-launderer, a finance geek who has left the big bank for whom he worked. In real life, however, we now know that this would be no freelancer; this would be the man from the bank itself, in suit and tie, protected all the way to the top. The scandal and outrage of major high street banks laundering Mexican drug cartel money has made headlines recently: American Wachovia and British HSBC were the first to be named and shamed – with more on the way – but the typical fines in such cases fall well short of proper punishment.

The banks' direct connections to the cartels' bloody war and the misery of drugs inevitably causes Stone to reflect on his two films about what was once his father's business, in those distant days when, he says "a bank was something that you saved with, and gave you a loan". He says of the money-laundering: "You kind of get a sense of where the real power lies. Gekko [his character in Wall Street] was an 1980s creature. But by 2008-9, the banks had changed. What Gekko was doing in the 1980s, everyone was doing – rigging things, fixing things – the outsider Gekko had become the system. Look at them! Making money with the money they took from the public, and gambling with it! You have these huge settlements, with AIG underwriting Goldman Sachs – and it's all over New York, that level of confidence, that level of arrogance and impunity. You go to the Hamptons, and you feel it." And there is an inevitable connection between this financial elite and the corporatisation of government.

"The United States," he says, "has been a corporate-controlled country increasingly since world war two. The concept of a national security state plays into that concept of us as a mega-corporation. I view the Pentagon as essentially a huge corporation. The United States has moved into corporate gridlock, and the gridlock controls us – the power of the lobbyists, banks, oil companies, pharmaceuticals … After Reagan triumphed in 1980, we had this embrace of the free market. But it's not a free market really, it's fixed. Because monopolies tend to dominate it, they come to the fore and push everybody out of the way. So it's a rigged playing field, like we saw in 2008 – the banks getting bigger and bigger.

"And you know the weird thing?" he asks, as if to the street below, those around the Brandenburg Gate. "Everyone wants to buy into that shit! The people take their cue from whoever has the power and the money! Go into the Four Seasons in New York, and power is the hero! No one wanted to talk about the poor Vietnamese when this all started, or the poor people in Latin America – no, we embrace power!"

He goes on: "I don't think Americans give a shit about out there. They don't understand why in the Middle East everyone hates America. They don't understand the 'backyard'. JFK did, and so did Henry Wallace when he was vice-president. They both tried to turn it round – and what happened? As soon as JFK was assassinated, Lyndon Johnson said he'd crank it up in Vietnam. In Latin America it was: 'Enough of this Alliance for Progress' shit, what about the $9bn we've got invested down there?'"

Which brings Stone to another subject he wants to talk about; for it never rains, it only pours with this tempest of a man. As Savages premieres, get ready – at the end of this month – for the publication of his book and thereafter the 10-part television series (to be shown in Britain next year) on which it is based, The Untold History of the United States. Working with the American University historian Peter Kuznick, Stone has compiled a series which, he says "is inspired by your British series The World at War – pure narrative, no talking heads and actors to portray some of the players. Ten one-hour programmes; everything's been fact-checked and now CBS has a copy. It's an unorthodox, true global story about America. About how Truman did not have to drop the atomic bomb that all the kids get taught was dropped to save lives and stop the war. That isn't why it happened, it was so that the world would become a huge amphitheatre for America. It's about the true origins of the cold war, which we all think was started by the Russians when they invaded eastern Europe (he gestures towards the window again, sun glinting off an S-Bahn train trundling through the glorious iron-and-glass station at Friedrichstrasse – not long ago, the overground platforms were in East Berlin; the underground ones were an interchange for the West Berlin U-Bahn system).

"It's about Truman after the war, a small man, a cold warrior and a political hack. After the war, we tried to demobilise, but it didn't last long. They created this legacy of rightwingers who pulled at this alarm that we were falling behind the Russians. But the Russians never achieved anything like parity – maybe at the end of the 1970s, but it broke them."

This is not history for history's sake, however – this is the history of our present and future, long beyond cold war, into war on terror, war on drugs: "It's the history," says Stone, "of our building the national security state, which is interested in nobody's security apart from that of the state. Always supposedly falling behind the enemy, so there would be no end to it. It's a legacy thing," he pleads, almost. "The American history our kids are reading is all upside down. Everything is the opposite to what you think." With Stone, a conversation can only return to the beginning – in the best sense – "because it is all interconnected", as are his films. But there is not time – though he does afford himself a valedictory thought that sends a shiver down the spine.

"This terror that we're supposed to be so terrified of … What the fuck is it? Why should we all be so scared? Well, there's big money in it, for sure. So now we have every form of technology at the disposal of the government and its war on terror – but who are we supposed to be terrified of? Why must we be so terrified?" For want of any further answers to his terrifying rhetorical question about being terrified of terror, Stone affords himself a joke, for like all good heretics, he is a jester too, at the court of America: "Jeezus!" He swallows a small bowl of salad dressing, neat, and rises from his chair. "The idea that the government is doing all this to protect me from marijuana!?"

Savages was released on 21 September. Amexica: War Along the Borderline