The ambush of a young man in his white Ferrari never looked like a run-of-the-mill murder. The arrival of a second group of gunmen to retrieve the body and the car, as police and reporters looked on, rammed home the point. The silence that followed made it crystal clear.

As far as the authorities and the local daily papers were concerned nothing happened that night in Culiacán, the capital of the Pacific coast state of Sinaloa and bastion of the Sinaloa cartel. As far as the tiny investigative local weekly Río Doce was concerned, it was time to get to work.

"It was just not right that they said nothing," says Ismael Bojórquez, the newspaper's editor. "People have a right to know what is going on."

Run on a shoestring from a few rooms above a dentist's office in Culiacán, Río Doce is one of the last redoubts of investigative journalism on the frontline of Mexico's drug wars that have killed more than 50,000 people since President Felipe Calderón launched his crackdown on organised crime five years ago.

The deaths or disappearance of more than 40 journalists, probably because of their work in this period, together with the direct and indirect threats that abound in all the main hotspots, mean most regional media limit their coverage to superficial reporting of violent events and arrests. Often they only do that when there is an official statement to quote. In some areas, particularly where the Zetas cartel is strong, a near news blackout reigns.

Río Doce's willingness to go further than other local papers is not, however, foolhardy bravery. Covering the dynamics of the conflict in Sinaloa, and staying alive, requires a subtlety illustrated in the case of the 2010 sports car murder.

The assigned reporter first ruled out initial information that the missing body was Joaquín "El Chapo" Guzmán – the leader of the Sinaloa cartel and the most famous of Mexico's many kingpins. He then confirmed the victim was the son of a Chapo ally from Michoacán state, nicknamed El Animal. He also delved into El Animal's bloodthirsty reputation.

With this in mind the story, which appeared without a byline, focused on the official information vacuum, slipping in the key facts almost by the by. It named the victim but did not mention his father or the Chapo link. The comments posted underneath the piece on the internet filled in the blanks – Mexico's version of open journalism at work.

Even Río Doce's rivals are lavish in their praise. "What they do is a lighthouse in the ocean for us all," says Marco Santos, news editor of the local daily Noroeste.

While it consistently condemns the corrosive influence of the drug cartels, Río Doce's editorial line puts more emphasis on criticising the government offensive as misguided and counterproductive. This is a matter of survival as well as conviction. An angry politician can be dangerous, but irate capos are a bigger worry.

There are limits. Río Doce doesn't touch the personal lives of the relatives of major underworld figures or mention laundering operations and trafficking infrastructure that have not been made public before. Other than that, the paper's four permanent reporters and dozen or so independent contributors rely on their instincts to decide what lines not to cross. They also get feedback from their sources about how their stories play with those that might be inclined to seek revenge. These sources range from members of the cartels and the security forces to people who just happen to know stuff in a state where drug trafficking goes back many decades and pulses through all walks of life.

"We all know people who are involved," says a young man who, while pursuing an eminently respectable career himself, has close ties with important trafficking families dating from childhood.

The story of how one of his best friends, an assassin, got upset at being deleted from his chat after killing his uncle by mistake, appeared in the paper last year. The details were altered to protect his identity in a way that simply leaving out his name could not.

"Many of Mexico's problems come from everybody being afraid of powerful people," he says. "Río Doce is very brave."

Bojórquez, the editor, says that for the moment the risks are manageable within his commitment to the idea that journalism is pointless unless it informs.

"We are also motivated by the hope that things will get better," he adds. "Actually, it is more of a hope that hope exists because, to be honest, at the moment I don't see a way out."