Anabel Hernández’s book (first published in Spanish in 2016) rates as one of the most difficult I have encountered in a very long time. Difficult at every level: to believe, to take in the implications, to process the appalling violence and, sadly, in parts, simply to read.

On the surface, it is basically an investigation into another Mexican atrocity. But this is as important a book about the state of a nation as any you will find. If Hernández is right – and her evidence is formidable – for four years the government of president Enrique Peña Nieto has been openly, indeed aggressively, lying about the fate of 43 students who disappeared one evening in the town of Iguala. It has not just lied, but actively covered up a crime, using a level of brutality and torture that rivals any drug cartel. And while the newly elected president, Andrés Manuel López Obrador, has promised an independent inquiry, we should perhaps not hold our breath: the most disturbing part of Hernández’s message is that the years of corruption by drug cartels has left a stuttering democracy, ruled by complicit politicians, where the military operates completely according to its own rules. This resembles the Colombia of the 1990s, when the state and cartels had virtually merged.

The gangsters in the mountains are tightly bound to the criminals in suits who are driven in smart black cars to work

On 26 September 2014, a group of students from a teacher-training college set out on their annual trip to Mexico City to attend a demonstration commemorating another government atrocity: the 1968 Tlatelolco massacre, in which soldiers and police gunned down hundreds of innocent protesters. Just like every other year, these students from some of the poorest regions of Mexico set out to “commandeer” buses from local towns to get themselves there. These annual hijackings were disruptive but in the past rarely ended up in serious violence. The fallout was usually handled by local police.

In 2014, this annual rite of passage turned into a nightmare. For a couple of hours, sections of the town of Iguala turned into a battlefield, even drawing in a bus carrying a semi-professional football team on its way home from a match. Six people died, dozens were injured – and 43 students simply vanished. To a public long inured to massacres and cartel murders, it was this last outrage that struck home.

Over the next couple of months, the government, in the shape of the federal investigative authorities, established what it called the “historic truth” of the events that night. Its story was that the students had inadvertently hijacked a bus packed with heroin being smuggled by a cartel in cahoots with the local mayor, his wife and the local police. The “disappeared” students were handed over by the police to the cartel, executed and then burned in a quarry. Their ashes were disposed of in a river. The investigators, including senior figures in the president’s administration, were adamant that there was no involvement from federal agencies, all of whom have bases in the town: not the state police, nor the federal police and certainly not the army. Again and again, it was underlined that the “feds” only found out about events once the shootings were over and the students had disappeared.

Almost immediately, Hernández smelled a rat. She is one of a handful of astonishingly brave Mexican journalists who have risked their lives covering the war on drugs, in her case focusing on the role of politicians and the state. When I worked with her on a film about the infamous drug lord, “El Chapo” Guzmán, she was uncovering documents about the deals between the cartels and every level of government. She knows the gangsters in the mountains are tightly bound to the criminals in suits who live in Mexico City and are driven in smart black cars to work. The bankers; the lawyers; the politicians: the people who ensure that in Mexico you never know whose side anybody is on. Hernández lives with bodyguards. When she began this investigation she had fled the country after hooded armed men forced their way into her house. Amazingly, she returned home to write this book.

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First, in an article published in December 2014, she disproved the federal authorities’ claim that they had no involvement in events. The students came from a famously radical college at which peasant children are trained to go back into their communities to teach. For years, the government and its agencies have kept a close watch on its relationship to the various guerrilla groups that make parts of south-west Mexico ungovernable. She proved that they were at least tracking all the students’ movements that day.

Then in 2016, she published this account, which dismantles the official story completely. Her chapter headings tell the story: The First Cover-up; Manufacturing Guilty Parties; The Historical Falsehood; In Mexico’s Dungeons. What emerges is a terrifying picture of how all levels of government have worked to stand up a series of lies as their “historical truth”. She provides visceral descriptions of torture to confirm a story that is reminiscent of the dirty war in the Argentinian and Chilean dictatorships of the 70s.

The government “truth” is held together by the almost tangible fear that any witnesses feel after decades of violence. More than 100 people have been arrested; many are still in prisons. But faced with Hernández’s minute analysis, the discrepancies between their forced accounts, the contradictions of lies, are laid out in pummelling detail. She names the names: the soldiers and policemen who were out on the streets when they claim they were not. When she can, she names those responsible for the torture. Some of the documents she found have been posted online.

Unhappily, this meticulously detailed approach may render parts of the book impenetrable to the average reader. Few will have the will to track which bus was which, or remember which acronym stands for which federal body.

Hernández’s version is that the students were indeed unlucky in commandeering a bus packed with heroin. But this was no local story. She claims to have interviewed a high-ranking cartel figure who, when he heard that one of his shipments had been inadvertently hijacked by the students, simply called on his contacts in the army to recover his goods. She explains how senior army officers, with the support of the police and intelligence services, set about reclaiming the goods for the cartel and how everything spun out of control. The students were unfortunate witnesses, and so had to be “disappeared”. Further collateral to the drugs war. What followed is a horrendous cover-up that reaches right to the top. Her conclusions convince, even if the cartel boss who admits responsibility for the initial order to stop the students seems to escape too much scrutiny. Does he not know how or where the students were taken? Even now, no one can tell the grieving relatives.

There are now supporting accounts, including an international commission of inquiry, which raise many of the same questions and essentially support Hernández’s version of events, though the official media say she has no proof, and one paper called it “political fiction”. Frighteningly, at least one of her witnesses has since gone missing. The Peña Nieto administration clings to its version of the truth. Hernández’s achievement is to turn this fate of 43 disappeared students into the continuing story of a state out of control. Mexico is still a democracy, and the president-elect is genuinely offering a radical new agenda in dealing with the cartels. After reading this, though, one wonders how even the best-intentioned leader will be able to turn the tide.

Angus Macqueen has made numerous documentaries in Latin America.

• A Massacre in Mexico: The True Story Behind the Missing Forty-Three Students by Anabel Hernández (translated by John Washington) is published by Verso (£16.99). To order a copy for £14.61 go to guardianbookshop.com or call 0330 333 6846. Free UK p&p over £10, online orders only. Phone orders min p&p of £1.99