There are no bigger victims to the clichés surrounding Afghanistan than the Afghans themselves. Tragically, the country is infested by glib non-truisms bandied around by foreigners, many of which help perpetuate the conflict rather than untangle it. That Afghanistan is the “graveyard of empires” is the biggest lie of them all.

Until 1840 Afghanistan, repeatedly and easily overrun by invaders, was known more plausibly as the “highway of conquest”. Rather than being a graveyard of empires it is in fact the graveyard of the thousands of Afghans killed by empires, or by the interference of the country’s more powerful neighbours. Steve Coll was in a prime position to address the issue of regional interference in his latest book, Directorate S. The author rightly won a Pulitzer prize for Ghost Wars, which charted the CIA’s covert programmes in Afghanistan from the invasion of the Soviets in 1979 to the rise of Osama Bin Laden.

Directorate S, which takes over in 2001, is a sequel. Named after the department of Pakistan’s intelligence agency (the ISI) that oversaw operations – rivalling those of the CIA – in Afghanistan, the book was hoped to be the definitive account of all that followed as US policy in the country, so heavily driven by the interplay between intelligence agencies, veered from one crisis to the next. Yet this time the author has overextended himself, relying too much on the collation of documents by his researchers and less on his own analysis and reporting skills, which were such key ingredients of the success of Ghost Wars. The result is a disappointing, dense compilation of names and events in which key themes and evolving trends are often excluded, or smothered by a mass of raw detail. The reader is left wading through chapters, laden with the same question that has so often burdened foreign troops in Afghanistan: how did we end up here (and how do we get out)?

Some of the omissions are bizarre. Take the case of Humam al-Balawi, the Jordanian double agent who set up a meeting with his CIA handlers in December 2009 to brief them on a supposed intelligence breakthrough. Balawi, a doctor, claimed to have been appointed as the personal physician to Osama Bin Laden’s right-hand man, the Egyptian Ayman al-Zawahiri, chief of al-Qaeda operations at the time and today the head of the organisation. This momentarily made Balawi one of the CIA’s highest-value sources in the region, and caused such excitement that the agency’s director, Leon Panetta, hurried to the White House and briefed President Obama in person.

Yet Balawi had double-crossed the Americans. When he arrived for the rendezvous at a small, heavily fortified CIA compound on Afghanistan’s eastern border with Pakistan, he detonated a suicide vest, killing ten people, including five CIA officers. Among the dead was one of the agency’s top al-Qaeda specialists, Jennifer Matthews.

This cataclysmic counter-penetration was the heaviest single loss for the CIA in a quarter-century of operations. So it was only to be expected that Coll might devote some space to the incident. Yet he never mentions it at all. This omission, one of many, represents a critical failure in a book that held such high expectations.

The title suggests it will examine two of the most vital factors affecting the war in Afghanistan and Pakistan: the complex, enemy-of-choice, ally-of-necessity relationship between the ISI and CIA, and the ISI’s equally complicated relationship with the Taliban. Yet Directorate S gives scant space to the ISI compared to the swathes it cedes to walk-on, walk-off American officials, who do little to explain why Directorate S operators managed to give direct support to the Taliban while duping the US.

Coll is a skilled journalist with experience of Afghanistan. In Ghost Wars he clearly explained how, between them, the CIA and ISI managed to seed radicalised militants into the heart of the anti-Soviet resistance, with disastrous consequences. Directorate S lacks a similar structured argument.

It does have moments of flourish. Coll’s cold, dense detail lends itself extraordinarily well, for example, to the emblematic murder of Abdul Wali, an Afghan detainee beaten to death during repeated interrogation by CIA contractor David Passaro at a base in Kunar province in 2003. Coll uses this killing to examine the CIA’s own perverse deviation into the world of torture and pseudoscience, whereby some officers sought to control the minds of prisoners by interrogation techniques that rendered them into a state of “learned helplessness”: so wretched as to be beyond hope.

Similarly, he uses the 2012 insider killings of two US officers – both murdered by an Afghan soldier in heavily secured offices near the coalition command centre in Kabul – as another case study of an emerging war trend. His description lingers with the reader long after we leave General John Allen, the US commander in Afghanistan, kneeling in prayer beside the sprawled bodies of his dead men, dressed in full battle gear, just a short walk from his headquarters.

Yet too often Coll drops his catch. The extensively documented four-hour meeting in Afghanistan between the ISI’s then director-general Mahmud Ahmed and the Taliban’s Mullah Omar on 17 September 2001, for example, should have been the moment for the author to nail down the narrative exposing top-level Pakistani complicity with the Taliban insurgency. Multiple testimonies from those present describe Ahmed instructing Omar to fight on against the Americans. Indeed, the ISI dispatched specialist assets quickly to help Omar do so. Coll misses the significance of this, writing it up as little more than a meeting in which the ISI chief presented the Taliban with the US demand to hand over Bin Laden.

Iran, the fourth pillar in the US-Pakistan-Afghanistan relationship, gets barely a mention, despite Iran’s Qods Force – a branch of the Revolutionary Guard Corps – playing a vital role in the resurrection of the Taliban.

Directorate S is a confused first draft of history, with evidential gaps. The war in Afghanistan is not a clichéd spiral of violence generated by some national love of bloodshed. War there is not inevitable, but the result of specific foreign policies. Authors need acute focus in exposing these, if they are not themselves to contribute to the overall sense of muddle that feeds the conflict.

Anthony Loyd, a correspondent for the Times, has reported from Afghanistan and Pakistan for more than 22 years

Directorate S: the CIA and America’s Secret Wars in Afghanistan and Pakistan, 2001–2016

Steve Coll

Allen Lane, 784pp, £25