Entitled Junkie: Confessions of an Unredeemed Drug Addict and authored pseudonymously by "William Lee" (Burroughs' mother's maiden name – he didn't look too far for a nom de plume), the Ace original retailed for 35 cents, and as a "Double Book" was bound back-to-back with Narcotic Agent by Maurice Helbrant. The two-books-in-one format was not uncommon in 1950s America, but besides the obvious similarity in subject matter, AA Wyn, Burroughs' publisher, felt that he had to balance such an unapologetic account of drug addiction with an abridgement of the memoirs of a Federal Bureau of Narcotics agent, which originally appeared in 1941.

Since, in the hysterical, anti-drug culture of postwar America, potential censure could easily induce self-censorship, it's remarkable that Junky (as it was published under his own name) found a publisher at all. Despite its subhead, Wyn did think the book had a redemptive capability, as the protagonist made efforts to free himself of his addiction, but he also insisted that Burroughs preface the work with an autobiographical sketch that would explain to the reader how it was that someone such as himself – a Harvard graduate from a Social Register family – came to be a drug addict. Both Junkie and Narcotic Agent have covers of beautiful garishness, featuring 1950s damsels in distress. On the cover of Junkie a craggy-browed man is grabbing a blond lovely from behind; one of his arms is around her neck, while the other grasps her hand, within which is a paper package. The table beside them has been knocked in the fray, propelling a spoon, a hypodermic, and even a gas ring, into inner space.

This cover illustration is, in fact, just that: an illustration of a scene described by Burroughs in the book. "When my wife saw I was getting the habit again, she did something she had never done before. I was cooking up a shot two days after I'd connected with Old Ike. My wife grabbed the spoon and threw the junk on the floor. I slapped her twice across the face and she threw herself on the bed, sobbing … " That this uncredited and now forgotten hack artist should have chosen one of the few episodes featuring the protagonist's wife to use for the cover illustration represents one of those nastily serendipitous ironies that Burroughs himself almost always chose to view as evidence of the magical universe.

From double book to stand alone; from Ace Original to Penguin Modern Classic; from unredeemed confession to cult novel; from a cheap shocker to a refined taste – the history of this text in a strange way acts as an allegory of the way the heroin subculture Burroughs depicted has mutated, spread and engrafted itself with the corpus of the wider society, in the process irretrievably altering that on which it parasitises. Just as – if you turn to his glossary of junk lingo and jive talk – you will see how many arcane drug terms have metastasised into the vigorous language.

Burroughs wrote Junky on the very brink of a transformation in western culture. His junkies were creatures of the depression, many of whose addictions predated even the Harrison Act of 1922, which outlawed the sale of heroin and cocaine in the US. Burroughs viewed the postwar era as a Götterdämmerung and a convulsive re-evaluation of values. With his anomic inclinations and his Mandarin intellect, he was in a paradoxical position vis a vis the coming cultural revolution of the 1960s. An open homosexual and a drug addict, his quintessentially Midwestern libertarianism led him to eschew any command economy of ethics, while his personal inclinations meant he had to travel with distastefully socialist and liberal fellows. For Burroughs, the re-evaluation was both discount and markup, and perhaps it was this that made him such a great avatar of the emergent counterculture.

Janus-faced, and like some terminally cadaverous butler, Burroughs ushers in the new society of kicks for insight as well as kicks' sake. In the final paragraph of Junky he writes: "Kick is seeing things from a special angle. Kick is momentary freedom from the claims of the ageing, cautious, nagging, frightened flesh."

Let's return to that cover illustration with its portrayal of "William Lee" as Rock Hudson and his common-law wife, Joan Vollmer, as Kim Novak. When I say Burroughs himself must have regarded the illustration – if he thought of it at all – as evidence of the magical universe he conceived of as underpinning and interpenetrating our own, it is because the first draft of the book was completed in the months immediately preceding his killing of Vollmer on 6 September 1951 in Mexico City. Burroughs wrote in his 1985 foreword to Queer (which was completed in the year after Vollmer's death, but remained unpublished until 34 years later), "I am forced to the appalling conclusion that I would never have become a writer but for Joan's death, and to a realisation of the extent to which this event has motivated and formulated my writing."

Much has been written and even more conjectured about the killing. Burroughs himself described it as "the accidental shooting death"; and although he jumped bail, he was only convicted – in absentia by the Mexican court – of homicide. However, to my mind this rings false with the way he characterised his life, and his writing, thereafter: "I live with the constant threat of possession and the constant need to escape from possession, from Control." Burroughs saw the agent of possession implicated in the killing as external to him, "a definite entity". He went further, hypothesising that such an entity might devise the modern, psychological conception of possession as a function of the subject's own psyche: "since nothing is more dangerous to a possessor than being seen as a separate invading creature by the host it has invaded".

Personally, I think Burroughs' definition of "possession" was tantamount to an admission of intent. Certainly, the hypothesis of murderous impulsiveness squares better with the impromptu "William Tell act" (whereby he called upon Vollmer to place a glass upon her head, which he would then shoot off) than his own bewilderment in the face of an act of such cruel stupidity and fatal rashness. (He knew the gun to shoot low, and what would have happened to the glass shards even if he had succeeded? There were others in the room.)

I belabour these events for two reasons. First, because I think an understanding of the milieu within which Burroughs and Vollmer operated, and the nature of their life together, is essential in disentangling the post hoc mythologising of the writer and his life from the very grim reality of active drug addiction that constitutes the action of Junky. When Burroughs was off heroin he was a bad, blackout drunk (for evidence you need look no further than his own confirmation in Junky). However much he cared for Vollmer, their life together was clearly at an impasse (their sexuality was incompatible and she was even beginning to object to his drug use); and what could be more natural – if only momentarily – than to conceive of ridding himself of an obvious blockage?

The original cover of Junkie by William Lee

Second, although the bulk of Junky was in place before the killing, Burroughs continued to revise the text at least as late as July 1952, including current events such as the arrival from New York of his old heroin-dealing partner Bill Garver (whose name is changed to "Bill Gains" in the text). The meat of the text of Junky is as close as Burroughs could get to a factual account of his own experience of heroin. In a letter to Allen Ginsberg (who had worried that the book constituted a justification of Burroughs' addiction), he inveighed: "As a matter of fact the book is the only accurate account I ever read of the real horror of junk. But I don't mean it as justification or deterrent or anything but an accurate account of what I experienced while I was on the junk. You might say it was a travel book more than anything else. It starts where I first make contact with junk, and it ends where no more contact is possible." All of which is by way of saying: Junky is not a novel at all, it is a memoir; "William Lee" and William Burroughs are one and the same person. Burroughs' own conception of himself was essentially fictional, and it's not superfluous to observe that before he began to write with any fixity he had already become a character in other writers' works, most notably in Jack Kerouac's On the Road. He also signed his letters to Ginsberg, Kerouac et al with his nom de plume, as well as using his correspondence as a form of work in progress, peppering his epistles to the Beats with his trademark riffs and routines. By the time Burroughs was living in Tangier in the late 1950s, his sense of being little more than a cipher, or a fictional construct, had become so plangent that he practised the art of insubstantiality with true zeal, revelling in the moniker "El Hombre Invisible".

Burroughs was the perfect incarnation of late 20th-century western angst precisely because he was an addict. Self-deluding, vain, narcissistic, self-obsessed, and yet curiously perceptive about the sickness of the world if not his own malaise, Burroughs both offered up and was compelled to provide his psyche as a form of Petri dish, within which were cultured the obsessive and compulsive viruses of modernity.

Burroughs never managed to recover from his addiction at all, and died in 1997 physically dependent on the synthetic opiate methadone. I find this a delicious irony: the great hero of freedom from social restraint, himself in bondage to a drug originally synthesised by Nazi chemists, and dubbed "Dolophine" in honour of the Fuhrer; the fearless libertarian expiring in the arms of an ersatz Morpheus, actively promoted by the federal government as a "cure" for heroin addiction. In the prologue to Junky and the introduction to The Naked Lunch, Burroughs writes of his own addiction as if it were a thing of the past, but this was never the case. In a thin-as-a-rake's progress that saw him move from America to Mexico, to Morocco, to France, to Britain, back to New York, and eventually to small-town Kansas, Burroughs was in flight either from the consequences of his chemical dependency, or seeking to avoid the drugs he craved.

As for the text itself, it reads today as fresh and unvarnished as it ever has. Burroughs' deadpan reportage owes as much to the hard-boiled style of the detective thriller writer Dashiell Hammett as it does to his more elevated philosophical inclinations. In eschewing rhetorical flourish or adjectival excess, Burroughs sought to remain silent about what could not be said, just like the drug subculture he was so enchanted by: "She shoved the package of weed at me. 'Take this and get out,' she said. 'You're both mother fuckers.' She was half asleep. Her voice was matter-of-fact as if referring to actual incest."

What it isn't is any kind of true analysis of the nature of addiction itself. Burroughs' own view – that "you become a narcotics addict because you do not have strong motivations in any other direction. Junk wins by default" – is a deceptively thin, Pandora's portfolio of an idea that raises the question: for what kind of person could drug addiction represent a "strong motivation"? Surely only one for whom alienation, and a lack of either moral or spiritual direction, was inbuilt.

Indeed, this is the great sadness of Junky (and Burroughs himself) as I conceive it. You can reread this entire text, assuming the hypothesis of addiction as a latent pathology, present in the individual prior to his having any direct experience of chemical dependency, and everything that Burroughs says about habitual heroin use begins to make perfect sense. But taking him at his own, self-justifying estimation (predicated on a renunciation of drugs that never came), Burroughs' Junky becomes the very archetype of the romanticisation of excess that has so typified our era: "I loosened the tie, and the dropper emptied into my vein. Coke hit my head, a pleasant dizziness and tension, while the morphine spread through my body in relaxing waves. 'Was that alright?' asked Ike, smiling. 'If God made anything better, he kept it for himself,' I said."

It is Burroughs' own denial of the nature of his addiction that makes this book capable of being read as a fiendish parable of modern alienation. For, in describing addiction as "a way of life", Burroughs makes of the hypodermic a microscope, through which he can examine the soul of man under late 20th-century capitalism. His descriptions of the "junk territories" his alter ego inhabits are, in fact, depictions of urban alienation itself. And just as in these areas junk is "a ghost in daylight on a crowded street", so his junkie characters - who are invariably described as "invisible", "dematerialized" and "boneless" - are, like the pseudonymous "William Lee" himself, the sentient residue left behind when the soul has been cooked up and injected into space.