The former five-star general and victorious military commander from World War II, Eisenhower was, in some ways, a contradiction: a career soldier with an abiding belief in peace. Early in his presidency, in 1953, he had said: "Every gun that is made, every warship launched, every rocket fired, signifies, in the final sense, a theft from those who hunger and are not fed, those who are cold and are not clothed."

The fateful 1960 election, which saw youthful Democrat Kennedy narrowly defeat Eisenhower's vice-president, Richard Nixon, is seen as a turning point: the oldest American president in a century was about to hand over to the youngest elected president. In popular culture depiction, the greying war veterans and Cold War activists mired in the past were making way for a bright, youthful, energised world focused on a glorious and boundless future.

Yet, as time passes, the cautious Eisenhower is increasingly seen as a wise – and justifiably worried – leader who steered the country through a tense period, avoiding many potential conflicts that could so easily have ignited another world war. He was also uncannily prescient.

In his televised farewell address to the nation on January 17, 1961, Eisenhower ranged over his eight years in office, but it was his reference to "the military-industrial complex" – a term he's credited with coining – for which that speech is remembered. He warned that the growth of the armaments industry and its influence posed a threat to public policy being subverted to serving the industry's interests rather than the public interest. While acknowledging the very real needs for national security, Eisenhower was concerned that this new military-industrial complex could weaken or destroy the very institutions and principles it was designed to protect. (Interestingly, he had originally intended calling it the military-industrial-congressional complex – signalling a concern about penetration of the legislature by lobbyists – but had been persuaded against it.)

His words were blunt: "This conjunction of an immense military establishment and a large arms industry is new in the American experience. The total influence – economic, political, even spiritual – is felt in every city, every state house, every office of the federal government. We recognise the imperative need for this development. Yet we must not fail to comprehend its grave implications. Our toil, resources and livelihood are all involved; so is the very structure of our society.

"In the councils of government, we must guard against the acquisition of unwarranted influence, whether sought or unsought, by the military-industrial complex. The potential for the disastrous rise of misplaced power exists and will persist. We must never let the weight of this combination endanger our liberties or democratic processes ..."

The idea came as a shock to many Americans, and Eisenhower was criticised in some quarters for being too negative. But to some long-term observers, growing domestic threats to American democracy and its institutions had long been apparent, but not necessarily from the source identified by Eisenhower. In a classic example of what historian Richard Hofstadter would later label the paranoid style in American politics, a Republican senator from Indiana, William Jenner, warned in 1954: "Outwardly, we have a constitutional government. We have operating within our government and political system, another body representing another form of government, a bureaucratic elite which believes our constitution is outmoded and is sure that it is the winning side ... All the strange developments in foreign policy agreements may be traced to this group, who are going to make us over to suit their pleasure ..." Jenner was hinting at communist subversion.

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The "military-industrial complex" of Eisenhower didn't disappear; on the contrary, it expanded exponentially, embracing the oil industry, the intelligence community, the national security agencies, Wall Street and, more recently, the strategically crucial Silicon Valley, morphing into what has been called "the deep state" – an officially unacknowledged second order of government behind the public or constitutional state that has grown significantly stronger since World War II. Unelected, unaccountable and, to all intents and purposes, utterly unconstrained.

While the notion, scope and reach of the deep state have long occupied the minds of conspiracy theorists of widely varying degrees of credibility and across the political spectrum, there has nevertheless been mounting evidence to suggest that certain elements of what constitutes the deep state have engaged in unlawful, even criminal, activities.

In the years immediately after World War II, the newly-formed Central Intelligence Agency joined forces with Corsican criminal syndicates in the French port of Marseille in efforts to dislodge communists from key trade unions. According to the respected historian, Alfred W. McCoy, who taught at the University of NSW in the 1970s, the CIA supplied the Corsicans with arms, money and disinformation. In his The Politics of Heroin in Southeast Asia, McCoy describes how the Corsicans gained political influence and control over the docks – ideal conditions for cementing a long-term partnership with mafia drug distributors, eventually turning Marseille into the postwar heroin capital of the Western world. Marseille's first heroin laboratories were opened in 1951, only months after the Corsicans took over the waterfront.

Into the 1960s, with the Vietnam War, the CIA airline, Air America, flew opium and heroin throughout the region, with many service personnel becoming addicts. A laboratory built at CIA headquarters in northern Laos was used to refine heroin. After a decade of American military intervention, South-East Asia had become the source of 70 per cent of the world's illicit opium and the major supplier of raw materials for America's booming heroin market.

Australia was not untouched, with the shadowy Nugan Hand Bank in Sydney a CIA bank in all but name. Jonathan Kwitny, in his 1987 book, The Crimes of Patriots: A True Tale of Dope, Dirty Money and the CIA, details how Nugan Hand financed drug trafficking, money laundering and international arms dealings, before collapsing in 1980, amid several mysterious deaths, and $50 million in debt. Among its officers were a network of US generals, admirals and CIA men, including former CIA director William Colby, who was also one of its lawyers.

From the Iran-Contra deals of the 1980s, through the various conflicts in Latin America and the Middle East, the CIA continued unchecked. In 1989, the United States invaded Panama, deposing General Manuel Noriega, who had been giving military assistance to Contra groups in Nicaragua at the US's request – which, in exchange, allowed him to continue his drug-trafficking activities – which they had known about since the 1960s. According to Alexander Cockburn and Jeffrey St. Clair in their 1998 book, Whiteout: The CIA, Drugs and the Press, when the US Drug Enforcement Administration tried to indict Noriega in 1971, the CIA prevented it from doing so.

In 1989, a Senate inquiry into America's involvement in the drug trade chaired by John Kerry, recently US secretary of state, found the US State Department had paid drug traffickers with funds authorised by Congress for "humanitarian assistance to the Contras", although little came of it.

Interest in the deep state continued to intensify, with a focus shifting to domestic activities. According to a series of reports by the San Jose Mercury News, for the better part of a decade, a San Francisco Bay Area drug ring, comprised of CIA and US Drug Enforcement Agency agents and informants, sold tonnes of cocaine to the Crips and Bloods street gangs of Los Angeles. Millions of dollars in drug profits were then funnelled to the Fuerza Democratica Nicaraguense (Nicaraguan Democratic Force), the largest of several anti-communist groups collectively known as the Contras.

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Last year, a former Republican staffer, Mike Lofgren, published a book that quickly became a best seller, The Deep State: The Fall of the Constitution and the Rise of a Shadow Government. He wrote: "[T]he deep state is so heavily entrenched, so well protected by surveillance, firepower, money and its ability to co-opt resistance that it is almost impervious to change ... If there is anything the deep state requires, it is silent, uninterrupted cash flow and the confidence that things will go on as they have in the past."

Also last year, another book, The American Deep State: Wall Street, Big Oil, and the Attack on US Democracy, by political analyst Peter Dale Scott, traces America's increasing militarisation, restrictions on constitutional rights, and income disparity since the Vietnam War. Scott argues that a major role in what he calls "this historic reversal" was the intervention of a series of structural deep events, ranging from the assassination of Kennedy to the September 11 attacks. While he doesn't try to resolve the controversies surrounding these events, he shows they share significant points in common, ranging from overlapping personnel and modes of operation to shared sources of funding.

The existence of the deep state, it can be assumed, has been known to all American presidents, some of whom have benefited politically. From Kennedy to Barack Obama, a tacit set of constraints has limited a president's scope for action. But where does Donald Trump, the outsider who pledged to drain the Washington swamp, sit in relation to the deep state? What was really behind the FBI's intervention in the campaign that was seen to benefit Trump?

Just where Trump stands on key issues – and how malleable he might be – is as intriguing to those who became insiders as well as everyone else. Steve Bannon, the right-wing Breitbart News chief who headed Trump's campaign and has since become the chief White House strategist and, more controversially, a member of the powerful National Security Council, told Vanity Fare magazine last year that Trump was, in terms of a right-wing agenda, a "blunt instrument for us ... I don't know whether he really gets it or not". (The comment carries echoes of the story, possibly apocryphal, circulating at the time of George W. Bush's candidacy for the Republican nomination for the 2000 election, when he was vetted by a group of influential neoconservatives seeking to further their influence. "He is perfect," one was quoted as saying, in reference to Bush's ignorance.)

Two conflicting hypotheses suggest themselves. The first is that Trump is largely ignorant of the deep state, believing that he, as President, can run the US, and possibly much of the world, as he wishes, just like he runs his business empire. Such a scenario doesn't augur well for his presidency. The second hypothesis is that he's very much the deep state's man; that he's willing to do its bidding, and facilitate and not hinder its actions in any way – a scenario that spells global trouble.

If he's not yet part of the deep state, did he signal his willingness to co-opt it in his first act as President, when he made the pilgrimage to the CIA headquarters at Langley, Virginia, just outside Washington? His words to the assembled spooks – extraordinary even for hyperbole-addicted Trump – were part pep talk, part declaration of love and, frighteningly, part blank cheque.

"Nobody feels stronger about the CIA and the intelligence community than Donald Trump. Nobody. I am so behind you. You're going to get so much backing, you're going to ask: 'Please Mr. President don't give us so much backing.' We're gonna do great things. We have not used the real abilities we have, we've been restrained. We have to get rid of ISIS. Radical Islamic terrorism has to be eradicated off the face of the earth. It is evil. This is a level of evil that we haven't seen. You're going to do a phenomenal job, but you're going to end it. This is going to be one of the most important groups towards making us safe, toward making us winners again, toward ending all of the problems, the havoc and fear that this sick group of people has caused. I am with you 1000 per cent! I love you, I respect you, and you will be leading the charge."

Because Trump's approach to foreign policy – used in a loose sense – is both confused and opaque, it's difficult to project what his unrestraining (whatever that means) of the CIA will mean for the world.

On January 27, Trump visited the Pentagon, raising with his comments there just the sort of concerns that Eisenhower had talked about almost six decades ago, hinting at preparation for permanent war. He issued an executive action calling for stepped-up military action in Syria and a vast expansion of the US military, including its nuclear arsenal, to prepare for war with "near-peer competitors" – a reference to nuclear-armed China and Russia – and "regional challengers", such as, presumably, Iran. Eisenhower's ghost would have blanched to a whiter shade of nuclear pale at Trump's words: "I'm signing an executive action to begin a great rebuilding of the armed services of the United States," he said during the signing of the document titled Rebuilding the US Armed Forces.

Key players in the military-industrial complex/deep state constellation are well-represented in the Trump cabinet, most notably James Mattis (military) at the Pentagon, Steve Mnuchin (Wall Street) at the Treasury and Rex Tillerson (big oil) at the State Department. Certainly, Trump's favourite, White House chief of Staff Reince Priebus, is known to have close CIA connections, with former CIA operative Robert Steele going so far as to name him as a CIA mole. To what extent these and others in the inner circle influence the President in his relationship with the deep state remains to be seen – but predictions on likely courses of action at this stage remain difficult.

Jessica Mathews, a former president of the Carnegie Endowment for International Peace and a former State Department official, wrote in this week's The New York Review that "a dangerous moment" has arrived, with Trump appearing to dismiss the very fundamentals that have been shared by all three contendings school of international relations: the neoconservatives, liberal internationalists and realists. These are:

While conceding that Trump's foreign policy often seems to be a mixture of impulsiveness and ignorance, Mathew points to an underlying consistency, citing his 1987 open letter, as a paid announcement in major newspapers, headed: "There's nothing wrong with American foreign defence policy that a little backbone can't cure." In it, Trump complained that other nations "have been taking advantage of the United States", convincing the US to pay for their defence while "brilliantly" managing weak currencies against the dollar.

Had Western leaders paid attention to the rantings in Mein Kampf, they would have found out just what Adolf Hitler was thinking and planning to do long before he did it. Trump's thinking, for want of a better term, must be taken more seriously than it has.

He fails to realise, or even understand, how America's global interests have been defended and furthered by its alliances; they have not weakened Uncle Sam so much as enabled him to become such a global colossus. For example, NATO, first and foremost, was an anti-Soviet alliance designed to protect American interests and American capital stemming initially from the Marshall plan. It is a gross distortion and fanciful in the extreme to represent it as some sort of benevolent organisation. As that ultimate realist, Napoleon, once observed, only two levers move men: fear and self-interest.

The only thing that is certain is that nothing is certain any more. A favourite Trump tactic, which he has acknowledged in his accounts of his business career, is to use negotiating tactics that involve taking off the table issues that have previously been dealt with and renegotiating them to his advantage. Translating this into diplomacy will, almost certainly, have devastating consequences, especially so for a world already beset by seemingly intractable problems including slowing growth climate change, rogue nuclear states, terrorism, displaced populations and the fracturing of Europe.

An unrestrained and rampant deep state under a pliant president operating from an isolationist Fortress America is truly the stuff of nightmare.

Dr Norman Abjorensen is a visiting fellow at the Australian National University's Crawford School of Public Policy, and the author of The Manner of Their Going: Prime Ministerial Exits from Lyne to Abbott. He is currently writing a history of democracy. norman.abjorensen@anu.edu.au