Vicente Fox, the former president of Mexico, began his administration in 2000 with a popular festival. Felipe Calderón, who took over in 2006, began his with a show of military force. His affinity for uniforms, army brass bands and public events with the armed forces makes an overt connection between the military and the executive that was unusual in Mexican politics before his presidency.

In January 2007 in Apatzingán, Calderón had his picture taken in military uniform, with a five-star cap and the national emblem. In May, again in Apatzingán, another photo op: officers with armoured vehicles and grenade launchers confronted alleged drug traffickers. But this great publicity stunt worried some – drugs are supposed to be under police, not military, jurisdiction.

After his 2006 victory was greeted by massive demonstrations over allegations of electoral fraud, Calderón needed to make up for his lack of popular legitimacy. The drug war soon became the central theme of his government. Taking on organised crime – leaning heavily on the army, which helped him into office in the first place, and with financial support from the US – has given Calderón a legitimacy that he did not receive in the voting booth, while militarising politics has given him the tools to run the country using emergency measures normally reserved for wartime. Here Calderón followed much the same script used by George Bush after 9/11, when the US president made war the constituent power of a neoconservative order. But, instead of sending troops to Iraq or Afghanistan, the Mexican president has ordered them into the streets of their own country.

The army now virtually occupies communities throughout the country, carrying out functions that, under the constitution, are not the responsibility of the armed forces: it has set up checkpoints, de facto curfews and inspections. In what appears to be the pilot of a plan for the entire country, in several northern states there is a situation that resembles a state of siege – one never decreed by congress.

In the short term, the politicisation of public security has worked for the president. Surveys show relatively high approval ratings, although they have been falling in recent months. Drug trafficking existed before Calderón took office, but his handling of it – while successful in terms of his popularity – has been a disaster for security. The president launched a war without a plan, and without assessing the consequences. Now he does not know where to go.

Recently, Calderón announced that there was to be a debate on the legalisation of marijuana in Mexico, while adding that he himself is against legalisation. Many people, including the leader of the opposition Institutional Revolutionary party, warn that this is merely an attempt to distract attention from the main issue on the political agenda: the failure of the war on drugs.

Trafficking in Mexico is now a $5bn-a-year business. Half a million people – 150,000 armed – are employed in the production of marijuana, opium and amphetamines, and the transit of cocaine, with two cartels fighting for the routes and the markets. The networks of the drug lord, Joaquín "El Chapo" Guzmán are barely touched. He is on the Forbes list of the wealthiest men on the planet and in sixth place in Time's ranking of the most influential people of 2008.

When Calderón took office there was no indication that trafficking would increase as it has. But it was as if he had smashed open a hornets' nest. Violence became intractable, and almost 29,000 people have died since 2006.

Human and civil rights have been this war's other casualty, thanks to changes in legislation. If a public building is occupied as a protest, anti-drug laws are used to accuse union leaders of kidnapping people who are inside. Homes can now be searched without a warrant.

In parts of Mexico, violence has been unleashed against human rights activists, environmentalists and grassroots leaders. Raúl Lucas García and Manuel Ponce Ríos were violently murdered by police in 2009. Indigenous and poor, they were dedicated to defending the rights of indigenous peoples in their state of Guerrero, denouncing human rights violations and carrying out social welfare projects. In Guerrero, military forces have engaged in low intensity warfare whose tactics include stealing crops, raping women, extrajudicial killings and even forced sterilisation. Similar stories can be told in other parts of Mexico.

In the macabre list of beheaded corpses, unburied bodies and mass graves that newspapers report on a daily basis, the assassination of grassroots leaders barely figures. And when it does, it is difficult for the public to register the difference between those killed due to drug trafficking and those targeted for their political activism.

The president doesn't seem to care that the militarisation of politics leads to a degradation and a weakening of the political sphere. He seems little concerned with the fact that in the middle of a major economic crisis – with manufacturing at a virtual standstill, unemployment growing and the escape valve of emigration to the United States closed – Calderón's room for manoeuvre has diminished significantly. The only way out, according to his logic, is to intensify the war.