MORELIA, Mexico—In the beginning, and until a year ago, a drug cartel called the Knights Templar ruled over the peaks, valleys, and coastline of Michoacán, on the Pacific coast of southwestern Mexico. The Knights controlled not only the poppy and marijuana plantations, and the meth superlabs in the hills, and the cocaine routes up from the coast; they also controlled large shares of the lime and avocado crop, and, most important, they mined precious metals from the sierra and exported them to China.

The Knights took other liberties. They extorted protection money from local business owners, condoned the occasional kidnapping, and expropriated land and livestock. The cartel had infiltrated the local and state governments to the extent that there was no outlet for the buildup of popular resentment. Then, in February 2013, bands of men, many of them lime farmers, formed dozens of armed “self-defense guards” across the state to combat the Knights.

On closer inspection, some of their rifles were automatic weapons; not exactly the antiquated bolt-action shotguns that humble farmers are known to carry around these parts. Some of their pickup trucks looked pricey and new. There was, even then, a sense that criminal gangs with grievances against the Knights were taking advantage of public discontent, in some cases even pulling the strings.

Eleven months later, in January 2014, with vigilantes mounting ever bolder offensives against the cartel, the Mexican government stepped in. Newly elected President Enrique Peña Nieto sent thousands of Mexican Federal Police to pacify the disturbances in Michoacán, with a special focus on the lime-growing region known as Tierra Caliente. Michoacán was placed in federal trusteeship, and a federal prosecutor named Alfredo Castillo was appointed to administer justice, his power superseding that of local and state authorities.

Bold and decisive in the language of its proponents, an authoritarian throwback to the days of the viceroy under the king of Spain to its detractors, the Commission for the Safety and Internal Development of Michoacán was born. Its first order of business was to channel the vigilante activity into a newly minted Rural Police Force. Commissioner Castillo gave an ultimatum to the self-defense forces: Join with the government or else. Nearly all submitted voluntarily. There was a righteous minority that refused to submit, and the commission had them arrested and jailed.

For the people of Michoacán, the issue then, as now, is whom to trust. From the very beginning of its reign, the commission made overtures to the leaders of local mafias open to the prospect of an overthrow of the Knights. In Castillo’s first month as commissioner, a photo of him appeared in the daily newspaper Reforma with an infamous capo, known as El Abuelo, who is an enemy of the Knights Templar. El Abuelo and the commissioner were photographed together at a recruitment event for volunteers to the Rural Police Force in the village of Tepalcatepec.

Commissioner Castillo said the photo was misleading; he denied knowing who El Abuelo was. But Reforma dug up an old press release from 2009 in which Castillo’s employer, the Mexican Attorney General’s Office, refers to the same individual as “the boss of the plaza of the village of Tepalcatepec, Michoacán.” El Abuelo turned up in another photo at a press event three months later; this time he was photographed standing in the ranks of the new Rural Police Force of Tepalcatepec. The commission denied that the capo, who has a criminal record of drug and weapons charges, was a member of the Rural Police. But a picture is worth a thousand words, and El Abuelo scooted away in an SUV immediately after the press event, not stopping to answer any questions.

The elected mayor of Tepalcatepec, Guillermo Valencia Reyes, says he was forced to leave town around this time because El Abuelo sent a team of commandos to city hall with a message that he was no longer welcome. Mayor Valencia fled the capital of Morelia, where he was living in hiding when he learned the city council had replaced him in what he called an illegal maneuver endorsed by Commissioner Castillo.

“I was replaced by a town councilman named Sergio Rodriguez Mora, a close associate of El Abuelo Farias,” Valenica told The Daily Beast. “I live in exile. It’s like they carried out a coup d’état, and the federal government will provide me no protection.”

El Abuelo is not the only dubious company the commission has been keeping. In May 2014, video appeared showing a commander of the Rural Police Force in the town of Buenavista meeting with the leader of the Knights Templar. The commission removed the commander, whose alias is Simon El Americano, from his post but reinstated him three months later. By way of explanation, the commissioner said the man in the video was not Simon El Americano. Reporters who covered the story told The Daily Beast that El Americano broke away from the Knights during the initial wave of disturbances in the state.

“The commissioner went to every county in the state and did the same thing,” Valencia said. “He met with the criminals. He empowered them, he gave them weapons, he gave them uniforms, he gave them resources like pickup trucks, and he put them under his orders, while permitting them to continue looking after their own criminal interests.”

Nothing quiets criticism quite like success. In 10 months, the Rural Police Force, together with the Federal Police, killed or captured a dozen of the most feared leaders of the Knights Templar. The only major capo still on the lam is the leader of leaders, Servando Martínez, aka La Tuta. Not only gangsters but the gangsters’ friends in politics went down as well: An ex-interim governor of the state, a governor’s son, the mayors of Apatzingán, Lázaro Cárdenas, Huetamo, Patzcuaro, Aguililla, and Tacámbaro, among others, are behind bars. A million tons of illegally extracted minerals were seized, along with 50,000 tons of illegally logged wood.

The problem now is that the Rural Police Force has itself become a bastion, not only for gangsters hostile to the Knights but for lower-ranking Knights themselves, sneeringly referred to among the ranks as “the repentant ones.” The term “legitimate self-defense force” was coined as a way to distinguish from corrupt elements within the Rural Police Force.

A YouTube video posted on Sept. 30 announced that self-defense forces were taking up arms again in the town of Aguililla. The reason, said the group’s founder, Jorge Vázquez, was the growth and consolidation of a dangerous cartel from out of state called Los Viagras, and, more specifically, the lack of a response from the commission to requests to arrest and jail members of this cartel.

Vazquéz said Los Viagras had infiltrated the Rural Police and were using the impunity of their badge and uniform to extort people all over Michoacán. He added that plenty of “repentant ones” who are part of the Rural Police continue to work for La Tuta, the cartel’s leader.

Today the security situation in Michoacán is unraveling quickly. The Rural Police as an entity is each day more openly derided by the citizenry as criminals. Sources in various parts of the state told The Daily Beast that criminals are everywhere. Historic feuds between villages and towns have escalated to bloody confrontations between heavily armed units of Rural Police. The commission appears to many to be losing its handle on the Rural Police Forces that were its own creation.

In November, the bodies of two commanders of the Rural Police were found decapitated in Uruapan. The commission will not confirm what locals are saying, that 11 members of the force were also disappeared. A month later, Simon El Americano led an assault against the Rural Police, his erstwhile comrades, in the neighboring town of La Ruana; 11 men were killed.

The leader of the Rural Police in La Ruana, Hipólito Mora, is a founder of the self-defense movement in Michoacán. Among the dead was his son. Mora and Simon El Americano are both in custody.

At a press conference, Commissioner Castillo stressed that the confrontation “was not against the government in the first place nor was it against organized crime but rather had to do with an internal division, which is why I have been emphatically stressing that what has happened has nothing at all to do with questions of public safety.”

In response to the killings in La Ruana, Castillo moved to disband the roving SWAT Unit of the Rural Police. The Rural Police Forces are now legally bound to remain in their towns and villages of origin.

A motley crew of protesters identifying variously as Rural Police and “legitimate self-defense forces,” in response to the killings and arrests in La Ruana, staged an unarmed takeover of city hall in the nearby city of Apatzingan.

At a press conference on Dec. 23, Commissioner Castillo had referred to them as “interest groups, some of a political nature, others with personal or group interests which seek to try to pressure under one pretext or another, and the focal point has been Apatzingan, which unlike any other place, Apatzingan was always under the yoke of organized crime, in particular the Knights, so there is a diversity of leaders who are seeking to assume power as the one who can truly guarantee the safety of the town.”

The democratic rights of the protesters, the commissioner added, will be respected so long as no crime is being committed.

At 3 a.m. on Jan. 6, Federal Police stormed the city hall in Apatzingan and ejected the protesters occupying the mayor’s office. The Federal Police seized a number of pickup trucks, which they claimed were reported stolen. Castillo reported one casualty during the expulsion, a protester who was run over by a truck while attempting to flee.

One eyewitness, a government official in Apatzingan, told The Daily Beast he suspected there were many more wounded than the commissioner acknowledged. “There had to have been gunshot wounds because there is blood all over the place and I saw it for myself. We know there were many wounded because there was blood all over the city hall.

The vehicles in question, the official said, were indeed stolen, with many stolen from members of the Knights Templar during the crackdown or prior months. He added that the Rural Police had separately been stealing trucks from ordinary citizens in the area.

A video shot at 8 a.m. that day from a telephone pole camera shows a formidable procession of Federal Police trucks escorting tow trucks that are transporting the repossessed trucks to the impound lot in Apatzingan. In a flash, 15 or so pickups stop short of the rear of the police procession and the men jump out of the trucks and go running after the police; they can be seen quickly reversing course and sprinting in the opposite direction.

The same local government official, who agreed to speak only on the condition that his identity remain a secret, said he lives two blocks from the second confrontation and was an eyewitness. He said the protesters were armed with sticks and stones, not firearms.

“I can tell you what I saw for myself right here on Constitution Avenue, where it all happened,” he said. “At approximately 7:45 a.m., we heard gunshots and we saw the people from the self-defense groups jump down from their trucks, and before you knew it they were screaming, ‘We’re unarmed, don’t shoot!’ and they put their hands up like that. And the police didn’t give a damn. They killed one poor kid right then and there. There were women and children around and they didn’t give a damn.

“They killed them all like that. One of them screamed, ‘Don’t shoot! We’re unarmed!’ Please don’t kill us!’ And they didn’t give a damn. Like it was all done on purpose, under orders. Disgusting. Worse than a shootout. This was a massacre.”

The official said there was a shocking amount of blood spilled on Constitution Avenue, and he put the death toll at 11 protesters, with many more likely wounded. The death toll is one of several points in dispute. Mayor Valencia set the number of dead at 15 or more. Padre Gregorio Lopez, an outspoken parish priest in Apatzingan, set it at “over 17.” Commissioner Castillo declared that nine were killed and said seven of those perished in “friendly fire.” The commission maintains the firefight was initiated by the protesters and that seven of the protesters died because, in effect, they shot each other.

In a separate video, shot some time after the confrontation, several victims can be seen lying in a circle around a stopped pickup truck. The truck is riddled with bullets, and the individuals lying around it appear to have been shot while attempting to escape from the cab and rear bed of the pickup. One of the men flails his arms about in a pool of blood; he is still alive. The crime scene has been cordoned off in yellow crime scene tape, but no official can be seen tending to the wounded man.

Commissioner Castillo responded to reporters’ inquiries on the subject by saying the Federal Police tended to the wounded as best they could, claiming there is video footage to attest to that. He said he could not answer for the tardiness of the paramedics.

But the eyewitness, who is a government official in Apatzingan, said the Federal Police prevented paramedics from reaching the scene of the crime and administering first aid:

“They said the bodies were not to be moved until they were surely dead. They corralled them while they were still alive and waited for them to bleed out.”

Commissioner Castillo was called to appear before the Mexican Congress on Jan. 13 to address the recent rise in violence. He told reporters in Morelia that he would be proud to appear before the legislators “to show them the actions and the pending actions we have taken in the state of Michoacán.”

On the same morning as Commissioner Castillo’s press conference, five self-defense force members were murdered and eight wounded in an ambush while on patrol in the municipality of Aquila, on the Pacific coast. Among the self-defense members killed was the commander of self-defense forces in the indigenous village of Huahua. It was the second ambush in a month in the coastal region of the state.

It is election season in Michoacán, and the politicians from the opposition parties are stepping forward like never before to offer their harshest criticisms of Commissioner Castillo. Selene Vázquez Alatorre, a city councilwoman in Morelia running for governor with the left-of-center Citizen Movement party, referred to the commissioner as “a corrupt cop” and went so far as to accuse Castillo of working in league with criminal interests.

From his exile in Morelia, the constitutional mayor of Tepalcatepec, Guillermo Valencia, is working the phones to get the latest news about what is happening around the state. He says he is trying to put the recent violence in context.

“The context is that Commissioner Alfredo Castillo at first used these people, he used them, he authorized them, he gave them uniforms, he gave them firearms, and now that they don’t serve his interests anymore he is sacrificing them, murdering them, to foment divisions between them and take advantage of the divisions,” he said. “What they are doing is cleaning out the plaza for another cartel. So the commissioner made a pact with El Abuelo Farias, and that is what is going on in Michoacán.”