With the dashboard's electronic clock marking 2am, the car careered through the Complexo da Coréia, one of the city's largest and most notorious slums, home to around 60,000 Brazilians and the HQ of one of the city's three main drug factions, the Pure Third Command.

What would happen if we ran into the police? "They would open fire," Spiderman replied bluntly, his mouth half full with fluorescent pink candy. Welcome to the inner-sanctums of a murky underworld of murder, violence and solitude that is rarely seen by outsiders. Spiderman was conducting a guided tour of the sprawling slum where he was born, and where he was now in charge of the area's lucrative drug trade and the leader of 200-strong private militia of heavily-armed young men.

"The lives we lead – we know they aren't right," he stuttered, pulling up outside a local sweet shop so he could stock-up on candy. "But we're not knocking on anyone's door to sell them anything. Those who want drugs buy them. We don't sell them to children."

And how did he manage to control such a large area? "It's God!" he replied, without hesitation. "We know that God doesn't approve of selling drugs but, like I told you, everybody has their dreams of being happy."

Last month Rio exploded in celebrations after being awarded the 2016 Summer Olympic games. President Luiz Inácio Lula da Silva cried. Copacabana erupted in a hail of confetti. But the celebrations were short-lived. Two weeks later, the city was rattled by a new wave of urban violence after a police helicopter was shot down during a turf war between traffickers, killing three officers. The ensuing clashes between police and drug gangs took the body count to nearly 50.

If violence continues at current levels, thousands more will die before the 2016 summer Olympics.

One local NGO, the Observatório de Favelas, estimates that there will be another 40,000 homicides in Rio state before 2016. At least 6,000 people, mostly men, will be killed "resisting arrest" by the police, while more than 500 policemen are also likely to die. Dozens of innocent civilians will be killed in the crossfire.

With the state's presence in Rio's ganglands still largely restricted to sporadic police operations, a small army of evangelical preachers is left to pick up the pieces. Each week they drag young, bloodied men away from the drug traffickers and into their churches, and mediate informal truces between warring factions.

"The police have to invest in bullet-proof vehicles and rifles to get into these places," said Dione dos Santos, Spiderman's local preacher, who has convinced the drug lord to spare those who break his rules, as he set out from his church on another late-night preaching mission at a drug den in another large slum. "We go in with the Bible and the word of God."

The contact between evangelical preachers and Rio's gang members is spawning a new generation of evangelical traffickers – men who paint their communities with passages from the Bible and tattoo psalms on their bodies, but who fall silent when you ask them about the Fifth Commandment; men who burn their enemies in makeshift cemeteries or hack their bodies apart with axes, but who also plaster signs around their slums' playgrounds reading: "Don't smoke marijuana here. If you insist on it, you will be 'charged'."

"The favela I control has the word of God everywhere," claimed Márcio da Silva Lima, a drug kingpin better known as Tola, one of Rio's three most wanted men, who controls Vila Aliança, the slum next to Spiderman's. Tola said the evangelicals had helped to reduce violence in the slum he controlled by rescuing those who broke the traffickers' rules: don't rob, don't rape, don't talk.

'God Exists'

"Now of every 100 [who cross us], 99 survive. Even though we know that that person deserves to die," explained Tola, who has equipped his foot-soldiers not just with weapons, but with black baseball caps bearing his initials and the phrase: "God Exists".

Why? "A grenade exploded on me and I'm still alive. I got shot six times with a 762 assault rifle and I'm still alive. My AK-47 went off in my mouth and I'm still alive. It's not because I'm a hero. It's because God wants me alive. If it wasn't for God I would be dead," he said.

"All the kids here need to study, not to kill and sell drugs," Spiderman said during a meeting last year in Pastor Dione's church. "Because today I know – even with God protecting me – the risk I run of dying."

Rio's drug factions began to take root in the city's slums in the 1980s, partly as a result of hard-line drug policies introduced by the US government, which many believe helped to force the drug trade from North to South America. The following decade saw an influx of heavy weapons into the city's slums and the murder rate soared. Today there are more than 5,000 homicides in Rio state each year.

After decades of violence and economic stagnation, Rio's Olympic victory is seen as a major chance to revive the city's fortunes, and some analysts believe the tide is starting to turn, however slowly. The last 12 months have seen drug traffickers expelled from five of Rio's 1,000-odd slums after a permanent occupation by military police. Recent weeks have seen police commanders and security authorities handing out presents to children in the slums as part of a hearts and minds campaign designed to convince locals that the police are preferable to the traffickers.

This week, Rio state's governors announced plans to extend these "pacification projects" to another 37 slums, among them the Complexo da Coréia and Vila Aliança. But such communities remain the exception. Most are still controlled by elusive drug lords whose faces are normally only seen on wanted posters, or in grim trophy shots taken after they have been killed by police officers.

In the public imagination, the drug lords are often seen as wealthy mafiosos, surrounded by fast-cars, beautiful women and stacks of money. Travel into their territories, lives and homes, however, and it becomes clear that Rio's underworld is a place of solitude, paranoia and relentless violence.

"I know one day I'll have to pay for what I've done – whether that means one year, 10 years or 30 years," said Tola, as he sat on the porch of his family home on the western outskirts of Rio. "I'm not kidding myself." Outside, three male bodyguards loitered in the shadows, their hands gripped tightly around high calibre assault rifles.

"This is no kind of life," Tola went on, his baggy shorts revealing a badly mutilated left leg, the result of countless shoot-outs. "Having to kill people who were your friends, who have eaten off the same plate as you. Shit! What's that? That is no life. I'll never tell my son to pick up a rifle. Do you think I want him to go through what I'm going through? I haven't had a bath in two days."

Biblical mural

Last month, as Brazilian authorities commemorated Rio's Olympic success, Tola was awaiting trial in a high security prison not far from his favela. He was arrested in the Brazilian countryside in August, after fleeing the slum.

But the violence goes on. "Next week it could be me," wept Jacyr Ferreira dos Santos, a former political exile who spent time in Brighton during the 1964 dictatorship before returning to Brazil to enlist in the civil police drug squad. Ferreira was sitting on a curb in one of Rio's most violent slums and minutes earlier had witnessed his colleague's skull shattered by a high calibre rifle shot.

"We come here and we shoot and we get shot at … And then the time comes and we go home. And they stay here, killing. So why do we come here? If you have an answer for me, give me it, because I don't have one."

Back in the Complexo da Coréia, Spiderman's softly spoken mother, Maria, who came to Rio from Brazil's impoverished countryside in search of a better life, looked elsewhere for answers. "Only Jesus [can protect my son]," she said. "He's the only one."

On the wall behind her was a mural that Spiderman commissioned from a local artist, the previous year with the words from Psalm 91, verse seven. "A thousand shall fall at thy side, and ten thousand at thy right hand; but it shall not come nigh thee."

Six months later, on Friday 13 March this year, Spiderman was dead – killed in a hail of bullets by a unit of Rio's military police.

• This article was amended on 6 November 2009. The original referred to Rio de Janeiro as Brazil's capital. This has been corrected.

Dancing with the Devil, created and co-produced by Tom Phillips, will be shown on More 4 on 10 November at 10pm.