Oliver Stone got so sick of always reading the sanitised version of US history that he decided to write his own. He talks about the real reason America dropped the atom bomb, how Kennedy is a hero and why he can't stand Hillary Clinton

Oliver Stone has just agreed to take part in the US version of Jamie's Dream School, the TV show that explored the interesting notion that famous people might educate kids better than teachers. "It was much criticised in Britain but I still think it's a good idea," says Stone over coffee and bagels in a Soho hotel. He'll be the American equivalent of Jamie's history teacher David Starkey. Only, you'd suspect, more radical.

Stone's TV history class might well be named US Heresies 101. "We're going to take these texts from regular history and compare them to what we think happened." He will teach that the bombing of Hiroshima was premised on a lie, that the CIA's secret war against leftist Central American governments was based on chimerical communist threat, that the invasions of Afghanistan and Iraq were follies and, perhaps most intolerable of all to patriots, that the United States of America is just as self-serving, duplicitous, corrupt, oppressive, expansionist and racist as – there's no easy way to say this – the British empire.

In the 1960s, Stone was awarded a bronze star and a purple heart with oak leaf cluster for heroism in Vietnam. If he survives lynching by adolescent reality-show neo-cons, he should get another medal.

It will be the latest improbable chapter in the life story of a man raised as an Eisenhower Republican, who fought as a patriot in Vietnam and made his name in Hollywood writing such splashy, amoral screenplays as Scarface for Al Pacino, before becoming an Oscar-winning, Chávez-admiring Buddhist whom the Observer described as "one of the few committed men of the left working in mainstream American cinema". Today he tells me he is looking forward to attending the Subversive film festival in Croatia. Of course he is.

One reason Stone has mutated into concerned TV historian is because in 2011 the US federal government survey reported that only 12% of US high school students knew their country's history. Why is that? "My theory is history is boring because the horror stories are left out. What's left in is the sanitised Disney version – a triumphalist narrative. We kind of always win. And we're always right."

For the past five years, the 66-year-old director has been working with historian Peter Kuznick on the desanitised version, complete with horror stories. The result is a 10-hour TV series called The Untold History of the United States, and an allied 750-page book. Stone and Kuznick want to confound the idea that the US fulfilled the destiny expressed in 1630 by John Winthrop, English Puritan lawyer and one of New England's founders, namely that America's destiny was to become a divinely ordained "city on the hill" – a beacon for the rest of the world to follow.

"I was brought up with all that manifest destiny stuff when I was a kid," says Stone. "I was sleepwalking until I was 40." What catalysed him to make this documentary history was finding that the sanitised version of US history he had jettisoned was still being taught to his children. "The reasons given for the atomic bomb are, in my opinion, nefarious and disingenuous. But we bought it. Now my 17-year-old daughter goes to a school – a very good school – where they're still told that in the textbooks: 'Japan would not have surrendered. The bomb ended the war to save American lives.'"

Didn't President Harry S Truman argue that the bombing of Hiroshima spared the lives of thousands of GIs who would have otherwise died in an invasion of Japan in 1945? "That's bullshit," snaps Stone. "And there's a very practical reason it's bullshit – we couldn't have even mounted an invasion until November."

His and Kuznick's theory, then, is that the atomic bombing of civilians was aimed, not at securing Japanese surrender, but at shocking and awing Stalin. They believe that, had Hiroshima and Nagasaki not been bombed in August 1945 by the US, something more intolerable to both Japanese and American sensibilities would have happened – namely that the Red Army, which by August had already swept through Japanese-occupied Manchuria, would have invaded Japan. Stone imagines the scenario from a Japanese perspective: "The Japanese are terrified. These guys [ie Soviet troops] are beasts. They rape, they kill. They'd kill an emperor without thinking about it. Look what they did in Germany."

As for Truman's US, the threat of a rampant Soviet Union in the postwar Pacific rim was even more chilling. So nuking Japan was aimed at impressing the Soviets. The bombs, for Stone and Kuznick, didn't just kill thousands of innocents, but unleashed a nuclear arms race and the cold war.

The real reason for America dropping the atomic bomb on Nagasaki and Hiroshima (above) was to impress Stalin, claims Stone. Photograph: EPA

For Stone, the US has, ever since those two fateful days in August 1945, been in the malefic grip of the military and hegemonic delusions. It has postured as extending democratic ideals but rather has extended control across the globe by any means necessary, including covert CIA support for death squads, drone attacks and calamitous invasions.

"We were showing we're as barbaric as we can be. As ruthless as the Russians could be in Germany, we could be more ruthless. We had no problems dropping the atomic bomb on civilians – a devastating war crime. If the Germans had dropped that bomb and lost the war, that bomb would have been stigmatised for all time. There would have been some international agreement to control it." But, Stone and Kuznick argue, because the US used atomic bombs first and was dishonest about why it did so, that international agreement didn't happen: instead, Stone grew up under that threat of nuclear Armageddon.

This account, unsurprisingly, has enraged some US historians. Writing in the New York Review of Books, Sean Wilentz argued that Stone and Kuznick ignore scholarship that contradicts their assumptions. "It is hardly clear, for example, that the Japanese government was close to surrendering on the Allies' terms in the summer of 1945," writes Wilentz. "American analysts believed that, short of a bloody invasion of its shores, Japanese leaders would fight hard, holding out for a much milder negotiated settlement, which negates Stone and Kuznick's contention that Truman was misleading about his motive for using atomic bombs."

Arguably, though, Stone and Kuznick's contention is less readily confuted. In his recent biography of so-called father of the bomb, Robert Oppenheimer, for instance, Ray Monk http://www.guardian.co.uk/culture/2012/nov/09/ray-monk-life-in-writing reports that the only nuclear scientist to have resigned on principle from the Manhattan Project, Joseph Rotblat http://www.guardian.co.uk/science/2005/sep/02/obituaries.obituaries, did so when he realised that the atomic bomb was not to be used to defeat the Nazis but to cow their ostensible allies. Rotblat overheard the military director of the Manhattan Project, Lieutenant General Richard Groves, say at a wartime dinner party: "You realise of course that the main purpose of this project is to subdue the Russkies."

In any event, Stone and Kuznick's more intriguing task is to do counterfactual history. Their American history isn't untold, but rather a meditation on what could have – and, in their view, should – have, happened. What if, they wonder, Truman had not succeeded Franklin D Roosevelt as president in April 1945? What if, instead of choosing Truman – whom the pair psychopathologise as having unresolved "gender issues" and portray as weak, biddable and blustering ("To err is Truman," 1940s Republicans sneered) – as Roosevelt's vice-presidential candidate in the 1944 presidential election, the Democratic convention had once more chosen the now little-known Henry Wallace to be FDR's running mate?

Their contention is that if, after FDR died in April 1945, vice-president Wallace had succeeded, postwar world history would have been very different. "The bomb would not have been dropped with Wallace or Roosevelt as president, in my opinion," says Stone. "Not at all. Not a chance. They [the military] would have opposed Wallace, given him a hard time, but you can't force a president to drop a bomb. You just can't."

Given that Stone and Kuznick's revisionist American history starts from the idea that Truman lowered the US's moral threshold and many of his successors continued that descent, this is no small issue. The drama of that 1944 Democratic convention is one that Stone and Kuznick wrote as a Hitchcockian thriller in the late 1990s before deciding to make it, a decade later, the linchpin of their documentary. "Bush wasn't an aberration," says Stone of the two-term Republican president whom he savaged in his 2008 biopic W, "Bush is the climax to an American mindset that had started with Truman and accelerated after world war two."

Stone won military awards for his time as a soldier in Vietnam. He thinks Kennedy would not have committed US troops in south-east Asia. Photograph: Alfred Batungbacal/Time Life Pictures/Getty Images

He portrays Wallace as the man who could have spared the US its postwar debacles – the cold war, Vietnam, the "war on terror" – had he managed to get that vice-presidential nomination in 1944. Wallace was, in short, the good father snatched away when America needed him most.

It's hard not to think that Stone has told this story before. In his 1991 film JFK, he depicted President Kennedy as a peace-loving liberal taken from America by a murderous conservative conspiracy covered up by the Warren Commission. He and Kuznick write: "We do know that Kennedy had many enemies who deplored progressive change just as fervently as those who had blocked Henry Wallace in 1944 when he was trying to lead the United States and the world down a similar path to peace and prosperity." For them, Kennedy died resisting the forces that wanted to push him into war with the Soviet Union.

If you wanted to psychoanalyse Stone as he and Kuznick do Truman, you might well focus on his close relationship with his father and the traumatising impact of his parents' abrupt divorce when their only child was away at school in 1962. His father Louis, a stockbroker and non-practising Jew, had been married to Jacqueline, a Frenchwoman and non-practising Catholic. They divorced in the year that Kennedy faced down the Soviet threat over the Cuban missile crisis. The following year, JFK was killed in Dealey Plaza, becoming the lost father to a grieving nation.

For Stone, Kennedy was the guy who could have spared the US the debacle of Vietnam and ended the cold war. "It was just inconceivable that Kennedy would have said yes to ground troops in Vietnam. He'd said no to the military on Laos. He'd said no at the Bay of Pigs on air support. And no at the Cuban missile crisis – that's the greatest single act of human courage this world has ever witnessed with that much at stake."

John F Kennedy campaigning in 1960: 'Saying no at the Cuban missile crisis was the single greatest act of human courage this world has witnessed.' Photograph: Bettmann/Corbis

You could fit most of Stone's cinema into this Oedipal frame. His 1986 Vietnam movie Platoon explored his Vietnam war experiences, with Charlie Sheen's rookie grunt confronting two war-seasoned father figures, the good sergeant (Willem Dafoe) and the bad sergeant (Tom Berenger). In Wall Street, Charlie Sheen's ingenue trader is mentored by Michael Douglas's venal Gordon Gekko. Stone's 1995 Nixon biopic, starring Anthony Hopkins, could be taken as manichean flipside to JFK – the bad father undone at Watergate as the good father was slain in Dallas. The Untold History of the US is, perhaps, also worth an Oedipal reading – it's the latest rebellion against the conservative politics his dad installed in him.

"I was born a conservative," he says. "My father raised me Eisenhower Republican. I was very much fearful of the communist conspiracy to take over the world." That fear led him to fight in Vietnam. "I was a patriot. I really believed it." Didn't Vietnam radicalise you? "No. I came out of Vietnam bloodied but not really understanding the geopolitical realities.

"I wrote the screenplay for Born on the Fourth of July [his adaptation of the autobiography of disillusioned Vietnam vet Ron Kovic, which Stone eventually filmed in 1989 starring Tom Cruise] in 1976. Ron was shot, castrated, in a wheelchair. He was radicalised by Vietnam, but I wasn't."

It was witnessing what the US did covertly in Central America during the 80s that did the job. "The scales dropped from my eyes when I saw the American presence throughout Guatemala. We trained and funded the death squads of Guatemala, the elite troops who did a lot of the massacring. I saw what we did in El Salvador, Honduras and Nicaragua too. The ultimate goal was to stop the communists taking control of the region – breaching the Rio Grande, as Reagan said.

"I thought at the time, looking around: 'This is Vietnam redux.' I may be stupid, but it took me about 15 years to get it. I saw that America was this bully and I hated it. From then on, I made progressive films."

The first of those was Salvador (1986) about a cynical hack (James Woods) politically awakened by witnessing the military coup in El Salvador propelled by US-backed death squads. His subsequent career, right up to The Untold History of the United States, amounts to a retrospective critique of what he believed about the US until he was 40.

Hugo Chávez and Oliver Stone at the 2009 Venice film festival. Photograph: Pascal Le Segretain/Getty Images

Stone's version of American history ends on a hopeful note. How can you? "Well, Chávez was smiling as he was dying of horrible cancer because he kept on believing in something greater than himself. And I think we all do – those who care about the human race."

He takes succour from the Occupy movement and from Hillary Clinton being replaced as secretary of state. "I can't stand her!" he says. "She's been a hawk for years. She was against the Contras. She voted for the Iraq war. She urged Obama to send in more troops to Afghanistan. She's always taken the 'America is indispensable' routine and, most recently, she wrote an article for Foreign Affairs. She spoke of the 21st century as America's Pacific century, arguing that China can and should be contained. She's like those idiots on Fox News who make an enemy of China by presenting them as a threat. Who's the threat? We have 800 to 1,000 foreign bases; they have one."

Not that Stone lets the current US president off the hook. "Meanwhile, we have Obama spending $12bn over two years selling arms to Taiwan. We're putting arms into Vietnam and Australia. Ach," he says exasperatedly, "here we go again."

Stone is certainly more compelling as Cassandra than Pollyanna. He suggests the Pentagon is obsessed with "full-spectrum dominance". "It means we control air, land, sea, space and cyberspace. That's the plan. We've already attacked Iran with Israel with cybertools. Now we're truly seeking control of space. They're talking about drones 250 miles in space that can fire off laser blasts."

For Stone, these are delusions akin to Reagan's thwarted Star Wars dreams of the 1980s. He and Kuznick approvingly quote ex-Soviet premier Mikhail Gorbachev: "Everyone is used to America as the shepherd that tells everyone what to do. But this period has already ended." Not so much city on the hill, as city over the hill.

Nobody seems to have told the US, yet. Stone is upbeat: "In 15, 20 years, some young person is going to see The Untold History of the United States and it will maybe inspire the person who's going to lead the next generation. There's always hope."

Oliver Stone's Untold History of the United States starts on Sky Atlantic HD on Friday 19 April at 9pm.