Zherdevka, a dead-end town seven hours' drive from Moscow, is the sort of place where nothing ever happens. Almost all the cars are old, battered Ladas; the few cafés reek of cheap frying oil and are populated with friendly but tragic-faced people ordering large early morning glasses of vodka.

Amid this quiet provincial decay, an extraordinary drama has been unfolding in recent weeks, unseen to the world. On a bitter April morning under cold grey skies, two days after the start of the new trial of oligarch Mikhail Khodorkovsky in Moscow, six defendants were brought, amid heavy security, to a hearing in Zherdevka's small local courthouse.

Outwardly, the case is nothing special. Five men from Dagestan and Chechnya, Russia's restive Caucasus regions, are accused together with one ethnic Russian of an armed robbery which is alleged to have taken place early last year on a nearby stretch of road. But the Russian man on trial is no ordinary criminal. His name is Andrei Yakhnev, and until his arrest in early 2008 he was a high-ranking operative in Russia's secret war on terrorism.

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His friends and associates say there's no way he could have done it; his lawyer says the case against him is absurdly weak. People like Yakhnev are not usually put on trial for something as trifling as robbery in today's Russia. Even if he had committed the crime, his superiors, if they wanted to, would have had little problem in hushing up the whole affair and quietly releasing him. So why has he been left to rot in a provincial prison, facing a sentence of up to 12 years? Did he know too many secrets about his superiors? Did he get too close to a Russian-born British woman who has past links to Vladimir Putin's London-based enemies, and with whom he was having a cloak-and-dagger love affair?

Khodorkovsky is known across the world, but few people have heard the name of Andrei Yakhnev. While the trial of the former Yukos oil boss is taking place in the glare of the world's media, not a single journalist has covered Yakhnev's trial. But the background to his case reveals just as much about modern Russia as does the Khodorkovsky trial, providing a rare insight into the world of Russia's secret services straight from the pages of a John le Carré thriller. It's a dizzying tale of conspiracy theories, terrorists, secret agents, and a love affair across boundaries that are not normally crossed.

***

The slightly overweight, sleepy-eyed figure, hunched up inside a grey hoodie and perched on a wooden bench inside the metal cage at Zherdevka's courtroom, might not seem like a Russian Jason Bourne, but for more than a decade, that's exactly what he was; an elite field operative fluent in several languages sent on extremely dangerous top-secret missions.

Andrei Yakhnev was born in the southern Russian city of Mozdok in 1975, and after four years of training at a top military academy, he joined the Russian special forces, passing the rigorous selection process for the elite Vityaz unit – a section of the army specifically devoted to the fight against terrorism and often thrown into the front line of the Chechen wars on particularly dangerous missions. It was not possible to meet Yakhnev in prison, but through his lawyer he provided detailed answers to my questions, written from his cell, and starting with his biography.

According to Yakhnev's responses, he began his professional career as a deputy commander, and later commander of a counter-terrorism Vityaz company, thrown into combat situations with Chechen rebels. By 2001 he had moved into a role in the Interior Ministry that combined field operations with investigations and office-based intelligence work, and in 2003 he moved into a newly created special department of the ministry, T Centre. This department, one of the most secret in Russia, worked together with the state spy agency –the FSB – and was at the forefront of preventing terrorist attacks and investigating their aftermath.

Yakhnev held the rank of major, was due to be promoted to lieutenant-colonel in 2008, and his official title was "senior operative on very important matters", which, despite the comic book ring to it, meant that he was involved in the most important Interior Ministry missions. According to Andrei Soldatov, one of the leading independent experts on the Russian security services, this is the highest rank that it is possible for a field operative to hold. Yakhnev was a specialist in the Caucasus regions of Chechnya and Dagestan, the focal points of Muslim insurgency against Moscow's rule. In his written answers, he specifies that he also took part in missions in Belarus, Ukraine and Kazakhstan, as well as other countries "further abroad" which he declined to name. He speaks fluent English and Chechen.

"The FSB's task is to monitor suspicious activity, whereas the Interior Ministry had the task of carrying out missions to kill prominent terrorist leaders," says Soldatov, "special, top-secret groups, known internally by the abbreviation VSOG [temporary specialised operative groups] would be dispatched on missions to trouble-spots to eliminate terrorists and fighters. They were so secret that even the local Interior Ministry people wouldn't know about them, in order to prevent information leaks."

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Yakhnev had an identity card that would send shivers down the spine of any bribe-hungry traffic cop who happened to stop his BMW. The permit underlined his importance and said that nobody was allowed to search him or his car. Documents provided to the court also confirm that his work had given him several different number plates with which he could disguise his car, and those who know him suspect that he was given several fake passports on which to travel for missions abroad.

His job also involved office work and investigative duties, and his friends painted a picture of a man who was far more than just a hard-nosed killer.

"He is an incredibly intelligent and well-read guy," says Sergei Badamshin, a Moscow lawyer and friend of Yakhnev's. Most of Yakhnev's friends are too scared to talk, but Badamshin, a chatty man with a wry sense of humour, agrees to meet me late in the evening at a north Moscow café. The pair met through mutual acquaintances several years ago, and soon struck up a close friendship. "He made friends easily; everybody liked him. He was just as able to find a common language with oligarchs and paupers; generals or privates. Everyone saw him as an equal; he was just one of those people who you're immediately drawn to."

Yakhnev would disappear on long missions to the Caucasus, sometimes for several months, but when back in Moscow, the pair would meet up and unwind, hitting bars and clubs and making the most of the city's nightlife until the sun came up.

"Even when he was off duty, he would always have a weapon on him, a Stechkin pistol," says Badamshin. "I've only seen the man in a suit about twice, but he'd always have his gun. He was a real warrior. He didn't talk about the concrete missions he was on but it was obvious he was involved in big things."

On 19 January 2008, according to Yakhnev's responses, scrawled in the dark of his prison cell with black ballpoint pen on squared sheets of paper torn from an exercise book, he returned to Moscow from a mission in Dagestan that had lasted several months. He was given a week off, but on the night of 21 January was called in to help with an operation to track down and detain a bomb-maker from Karachayevo-Cherkessia, one of the southern Russian republics close to Chechnya, who was hiding in Moscow.

On 25 January, he received a call from Arsen Muidov, the man who acted as his ears in Moscow's Dagestani community, and whom he had used as an intelligence source since 1999. Muidov told Yakhnev that he had heard about a huge sum of money that was due to be transferred from Dagestan to Moscow – 25 million roubles (£500,000) in cash. This is where accounts diverge. According to the prosecution in the court case, Yakhnev agreed to become part of a criminal group with Muidov and others, to steal the money. According to Yakhnev himself, he agreed to drive to the meeting spot with Muidov and find out who was transporting the money and why. Because he didn't know where the money was from, he left a file on his desk at work, explaining where he was going and with what intelligence. A bit more than 24 hours later, he was under arrest.

"People with his kind of position; people with the documents that he had – those people don't end up behind bars in Russia," says Badamshin, who, as a lawyer, knows the country's court system well. Others who specialise in Russia's secret services agree. Russia's bureaucratic apparatus, and especially its secret elements, is notoriously corrupt, yet few important officials are held to account for making money on the side. If a high-ranking officer from the FSB or other secret services is put on trial in Russia, the reason for the criminal proceedings is usually to be found somewhere other than in the charges presented to the court.

So why is Andrei Yakhnev in prison?

***

Natalia Pelevine drags on slim cigarettes nervously as she talks. Pelevine is a garrulous 32-year-old woman with long hair, dyed jet-black, and a penchant for blood-red lipstick. In a series of meetings at Moscow cafés and restaurants during the past few months, she recounted her story in full for the first time.

"There was never any intention to go public with this, but it's got to the stage where there seems little other choice," she says. Tottering in high heels and wearing a bright purple jacket, she looks every inch the glamorous Russian woman, but w hen she speaks in English, the words come out in an Anglo-American lilt. Born in Moscow, she moved to London with her parents at the age of 11, just before the Soviet Union entered its death-throes. The family stayed in Britain, and Pelevine started a career as an actress, but returned frequently to Russia. She knew many Chechens in Moscow and followed with horror the Chechen wars of the 1990s. When Chechen rebels laid siege to a Moscow theatre in October 2002, she knew straight away that she wanted to write a play about it.

The Nord Ost siege, when hundreds of theatregoers were taken hostage by a heavily-armed gang of Chechens, was among the darkest hours of Vladimir Putin's eight-year presidency. The Russians pumped toxic gas into the theatre and thus avoided any explosions, but at least 130 hostages died, mostly because they were given no antidote to the gas. The Russian authorities presented the operation as a victory, but many survivors were angry that no proper investigation was ever held into the decisions taken to storm the theatre, and the apparent unpreparedness to deal with people who had been incapacitated by the gas.

Pelevine spent time in Moscow interviewing survivors of the attack and their relatives, making notes on how it had felt to be inside the theatre during the 57 hours of the siege. She met several times with Anna Politkovskaya, an investigative journalist who had written many articles on the siege and its aftermath. Wanting to know more about the decisions that had led to the storming of the theatre, she tried to set up interviews with people from the secret services who had been involved.

In the spring of 2005, she managed to secure a meeting with three retired FSB colonels who had been in the command centre during the siege. They met with Pelevine in the cafeteria of the Moscow city parliament, where one of the colonels, by then retired, had become an MP.

"They were very rude to me, asked me what I was trying to do by digging into this, and gave me absolutely nothing," says Pelevine. "It was more like them interviewing me than the other way round."

Indeed, along with a series of suspicious apartment block explosions in 1999 that preceded the second Chechen war and Vladimir Putin's rise to power, the events surrounding Nord Ost have always been something of a no-go area. The government investigation was cursory, and independent journalists who tried to get to the bottom of the story had a habit of meeting sticky ends.

Many things about the Nord Ost siege didn't seem to make sense. Why did the terrorists not blow themselves up when they realised that the theatre was being gassed? They had time before the deadly gas took effect to go out in a blaze of glory. Why did the special forces storming the building have an order to shoot to kill, not leaving a single terrorist alive for questioning? Why did the testimony from survivors suggest that the terrorists did not seem nervous and did not seem like they were ready to die – chatting to each other and painting their nails?

Six months after the siege, Anna Politkovskaya met with a Chechen man, Khanpash Terkibayev, who claimed that he had been part of the group that had staged the siege but had left before the storming of the theatre started. Terkibayev was a shadowy figure who had close links both to Chechen separatists and to top Kremlin officials, on occasion even travelling to Europe in official Russian delegations. Politkovskaya was certain that the Terkibayev story proved that at some level, elements in the secret services collaborated with the terrorists to abet the theatre siege.

Not long before Politkovskaya met with Terkibayev, the Russian politician Sergei Yushenkov was shot dead in Moscow. Alexander Litvinenko, a former FSB agent by then living in London, claimed to have passed a dossier on Terkibayev on to Yushenkov just a few days before his murder. Terkibayev died in a car crash in Chechnya in 2004. Politkovskaya was gunned down in the entrance of her apartment block in late 2006, just a few weeks before Litvinenko was poisoned with polonium and died in London.

There is no evidence that any of these deaths were related to Nord Ost investigations; Litvinenko and Politkovskaya were mired in a whole range of controversial topics, and there are persuasive alternative versions for Yushenkov's death. Terkibayev himself claimed that Politkovskaya had made the story up. Others note that the authorities were very sensitive about the details of the military operation at the theatre, keen to avoid what they saw as a victory being presented as a disaster; but most observers doubt that the FSB could have been involved in the preparations: "I never saw any evidence that would suggest the FSB was involved in any way with the organisation of Nord Ost," says Andrei Soldatov.

But what is certain is that nobody has ever carried out a proper independent investigation into what happened. Pelevine wanted to change that. In addition to her play, she began to plan a book about the events. "The more I investigated it, the more I realised it wasn't how it was made out to be," she says.

***

A contact in Moscow suggested that he might know someone who knew someone who had been involved in the government response to the siege. Phone calls were made, and a meeting place was agreed. After midnight one night in June 2005, says Pelevine, she was driven for about 40 minutes out of Moscow through darkened backstreets to a small restaurant tucked away in a wooded clearing. There were several tables outside, but no other people in sight. She sat down to wait with her contact, and after some time another car arrived and a big sturdy man with cropped sandy hair sat down across from her. It was Andrei Yakhnev.

He began to speak, quietly, without looking her in the eye. At that first meeting he didn't give away any major secrets about the way that the authorities handled Nord Ost, but he told her his side of the story with an honesty she hadn't encountered from anyone else who had been involved on the government side. Yakhnev had been in the command centre for part of the siege, and had entered the theatre during the storming. He had also been involved in the investigations that followed.

His story rang true and tallied with stories of victims of the siege, and in contrast to the dour FSB colonels she had questioned previously, Yakhnev was clearly emotionally involved in the tragedy and personally affected by it. Some of the things he told her seemed to reinforce suspicions that had been forming in her mind about what had really happened at Nord Ost.

The meeting moved Pelevine to tears, and she asked if she might take his contact number. He agreed, and the two said their goodbyes.

After a decent period of time had elapsed, she called Yakhnev and asked if they might meet again. The two began to meet on a regular basis and a friendship blossomed, based on mutual interests to start with, which in time turned into a romance. They spoke on the phone regularly but saw each other rarely. Pelevine was often away, in London or New York, and Yakhnev would go dark for days or weeks on end when he was out of Moscow on a mission. When they both happened to be in Moscow at the same time, he would call her and name a time and central Moscow location where they should meet. He would pick her up in his car and they'd spend a few hours together.

There was no doubt that the Russian authorities knew about the relationship between Andrei Yakhnev and Natalia Pelevine. They also almost certainly knew that Pelevine had links to figures in London that were committed to the overthrow of the Russian regime. Pelevine was close to many in the anti-Kremlin circle of Russian émigrés in the British capital, led by Boris Berezovsky, the oligarch who helped raise Putin to the presidency but then fell out of favour and fled. It was Akhmed Zakayev, the former Chechen rebel wanted by Moscow and currently living in Britain, who first introduced her to the group, after she had contacted him to talk about the play she was writing. Moscow has repeatedly demanded that Britain extradite both Berezovsky and Zakayev to face criminal proceedings in Russia, but the requests have been refused.

With Zakayev, Pelevine has remained on friendly terms, but she fell out with Berezovsky and his inner circle. "I believe his fight is all about personal vengeance rather than a desire to make this country better," she says. (Berezovsky was asked to comment on his relations with Pelevine through a London-based spokesman but did not respond.) The final break, says Pelevine, came when Alexander Litvinenko, with whom she had been acquainted, was murdered in London in late 2006. Pelevine suspected that there might be more to the story than met the eye at first glance.

But the falling-out was far in the future when Pelevine and Yakhnev's relationship started. The security services would have kept a close watch on a man in Yakhnev's position, and they certainly would have known about Pelevine and her links to Berezovsky. She was just the sort of person that the FSB would want to keep away from someone like Yakhnev. Why, then, did they allow the meetings to continue? It is possible that the Russian authorities told Yakhnev to keep the relationship going, curious to see if they had found a link to Berezovsky that could be exploited.

Amid what seemed to be the start of a serious relationship, both Pelevine and Yakhnev were always, at least partially, on their guard, never knowing if the other might have ulterior motives. Yakhnev may have suspected that Pelevine was a honeytrap, working for MI6 or Berezovsky and keen to glean as much information from him as possible not for the innocent project of writing a play about Nord Ost, but for darker purposes. Pelevine didn't know if Yakhnev had been told by his superiors to work her as a potential source on Berezovsky and Zakayev. The bizarre relationship continued. They seemed to be falling in love but, for obvious reasons, neither could fully trust the other.

Early one evening in the summer of 2006, according to Pelevine, Yakhnev called her and said they needed to meet at the Metropole, a swish, palatial hotel, a stone's throw from the Lubyanka, the infamous building where the KGB performed interrogations and executions, and which now serves as the headquarters of the FSB. He led her into the casino, and sat her down at a table in a side-bar where a man was reading a copy of Kommersant, one of Russia's leading daily newspapers. At several of the other tables, lone men were seated, and in the corner some musicians were playing mood music.

"Can we really talk here, with all these people around?" she asked him.

"It's OK, everyone here is one of us," replied Yakhnev, "Except the musicians." He gave a little laugh. "There is someone I need you to meet."

The third person at the table lowered his newspaper and introduced himself as a general lieutenant of the FSB, one of the top anti-terrorism officers in Russia's sprawling spy network. Yakhnev left. The general was drinking a coffee, and Pelevine ordered a white wine to calm her nerves.

"The whole set-up was ridiculous, like something out of a movie," recalls Pelevine. "He asked me, in a very jokey way, how long I had been working for MI6. I didn't know what to say, so I replied, in the same manner, that I'd been recruited while still at school." The conversation continued in a similar vein, with barbs disguised as jokes. She asked if he wanted to recruit her; he responded that they didn't just recruit anyone, but that she might just pass the test. He then asked if she realised the significance of being recorded as having met with him, and soon after told her to leave. She departed the meeting confused, scared, and furious with Yakhnev, and quickly left Moscow for London.

Something about the way they interacted with each other felt genuine, however, and the phone conversations, and then real-life meetings soon resumed. They had the same sporadic, hastily-arranged character as before. The meetings were intense, although it was rare that they could really be alone.

"The sexual life was pretty much non-existent; things only happened on a few occasions," says Pelevine. "He twice took me back to a flat that was extremely basic, with a bed, a small kitchen and an empty fridge. It was a place to recharge batteries, not to live." She never saw his real home or even knew where it was, nor did she even know his surname or how old he was. Those were questions that couldn't be asked.

What was clear was that they had found common ground. For Pelevine, it was refreshing to meet someone in Yakhnev's position who was so open and thoughtful about the consequences of his work. For Yakhnev, many of Pelevine's complaints about Russian policy in the Caucasus fell on understanding ears.

"I disagreed on the most fundamental issues," he writes, in response to the question of whether he approved of the way Russia was fighting against terrorism. "I always said that the people who participated in illegal terrorist forces in Chechnya and Dagestan did so for various reasons, and the same with those who supported them. I constantly told my superiors that to solve these problems we needed not punitive measures, but socio-economic ones. I also tried to explain that terrorists in Russia weren't financed from abroad, but by local political clans fighting for power in the north Caucasus republics, and wanting to secure power, administrative resources, and federal financing for themselves." In short, he completely disagreed with the official Russian line on terror in the Caucasus – that it was part of the international jihad movement and needed to be crushed mercilessly. He also noted with distaste that some of the generals who were supposed to be fighting terrorism seemed more concerned with enriching themselves than with protecting Russia's security.

One night in November 2007, the pair of them went for dinner at a restaurant near the Luzhniki Stadium in the south-west of Moscow. Yakhnev kept getting calls on his mobile phone and eventually they had to interrupt the meal and leave; it seemed he was being called onto a mission.

"He drove me back home, and as we were driving down Prospekt Mira, on the way to my apartment, he said, 'I'm thinking about leaving the service'," remembers Pelevine. "I said 'What? How is that even possible?' He asked me if I'd still be interested in him if he wasn't an agent, and I said that of course I would." Yakhnev dropped Pelevine off at her apartment, and disappeared off into the night, as he always did. It was the last time she saw him as a free man.

Aside from the research project about Nord Ost that had been germinating in Pelevine's mind, there was the initial undertaking that had got her interested in the theatre siege – the play. With the script finished in 2005, she asked around her friends in the Moscow theatre world, to see if it was possible to stage a production in the city. The script was controversial, with masked gunmen marauding down the aisles, and actors playing hostages scattered around the audience. Many people she spoke to thought it was a brave idea, but nobody wanted anything to do with it. Putting on a play like this in Russia, so soon after the siege, seemed like a dangerous idea. In the end, the play opened for a short run at the small New End Theatre in Hampstead, London, in the autumn of 2006. It received lukewarm reviews from British critics, but some of the Russian siege survivors flew to London for the premiere and were impressed. Coming from a country that tried its hardest to cover up the circumstances of the rescue operation, the victims were supportive of anything that would help keep the tragic events in the limelight.

Later, just before the arrest of Yakhnev, Pelevine heard through a friend that a Dagestani theatre director was interested to stage the play in Makhachkala, the capital of Dagestan and one of the most dangerous cities in Russia, where shoot-outs between Russian forces and militants occur on a frequent basis, and where some of Yakhnev's trickiest missions had been. It was a bold move to put on a play with this subject matter in such a place, but after negotiations, Pelevine wrote a Russian translation of the script and rehearsals began in earnest early in 2008, around the time of Yakhnev's arrest.

On 4 April, the day of the premiere, the cast and crew were told at the last minute that the president of Dagestan, Mukhu Aliyev, would be attending the performance with his entourage. Hasty negotiations were made for a post-performance banquet, and a clever individual thought to inform the president's security detail that the play featured actors dressed as terrorists. "Lucky you told us," said one, "or we would have shot them dead immediately."

For the premiere, Pelevine had flown into the city, which sits on the Caspian Sea, near the majestic peaks and valleys of the Caucasus, home to the militants whom Yakhnev had been tasked to exterminate. At 5.30pm, the performance started. At 7pm the curtain fell; videos of the performance show some of the audience in tears and many giving a standing ovation. But while the audience applauded, the Dagestani president got up and swept out of the theatre with his entourage of government officials and security. Shortly afterwards, the director got a phone call saying that the play should never be put on again. President Aliyev claimed the play glorified terrorism, and accused Pelevine of being part of a London-based plot to destabilise Dagestan.

Then, just minutes after the curtain fell on the play in Russia for the first and only time, an explosion tore through Pelevine's Moscow apartment block.

"I was on the phone to friends at Novaya Gazeta, telling them about what had happened with the play. They knew roughly where I lived, and asked what street my apartment was on. I told them. They asked the number of the apartment block. I told them. 'There's just been a bomb,' they said."

An explosion had ripped through neighbouring apartments, killing three and causing huge damage to the home of Pelevine's grandparents, where she stayed when she was in Moscow. (Her Russian passport bears a stamp stating that she is registered at that address.) Pelevine's grandparents were not injured. The city authorities initially claimed there had been a gas explosion; later it was revealed that it had indeed been a bomb. Two of her dead neighbours were linked with a far-right nationalist group whom, the authorities suggested, might have been trying to make an explosive device which had detonated by accident, killing them. Although the Russian far right does not have a history of using bombs, preferring fists and knives, this is the version of events that has been sustained until now, with no proper investigation into the incident.

As so often in Russia with events such as these, there is no way of knowing if there was more to the incident than the official explanation suggests. But bombs do not explode with regularity in Moscow; and the timing was suspicious, to say the least. A huge explosion, metres away from Pelevine's grandparents, just minutes after the curtain had fallen on the first night of her play; it seemed like a sign from someone that she should shut up and go away.

***

I first met Natalia Pelevine almost exactly a year ago. I had heard about the fate of her play in Dagestan and asked to meet her to discuss the details for an article about the play which later appeared in The Independent. We stayed in touch, and over time, she slowly began to reveal details about her relationship with Yakhnev and his arrest. To start with, it sounded fantastical, but the more I heard the more interested I became, and in early April I decided to travel to Zherdevka to see the court case for myself.

I hitched a ride with Vladimir Samarin, the lawyer representing Yakhnev, and we left Moscow the morning before the hearing in his blue Land Rover. As we drove south-east, through a monotonous pancake-flat landscape of birch trees sprouting like stubble from the last vestiges of the winter snow, he filled me in on the details of the trial so far.

Samarin, a wiry diminutive man, is an immensely likeable character, who likes to pepper his speech with jokey non-sequiturs. After years in the Soviet navy, working in underwater special operations in the Pacific, he trained as a lawyer in the 1990s, and appears to have struck up a personal bond with Yakhnev during his time on the case.

We arrived in Tambov, the drab regional capital, famous for little except creating one of Russia's most unpleasant mafia groupings, late in the afternoon. The pre-trial detention centre where Yakhnev was being held was here, and Samarin left me with a bowl of borscht in a cafe across the road while he went off to meet his client. While I slurped down the purple soup, a blonde girl in knee-high boots sung saccharine pop songs to the accompaniment of a Casio keyboard, and a few bored looking prostitutes sipped beers at the bar.

Early the next morning, we set off on the two-hour drive from Tambov to Zherdevka. En route, we passed the place where the armed robbery is meant to have taken place, a nondescript petrol station with a few blue-painted pumps and a small shop, just before the turn-off from the main road to Zherdevka. I would later receive answers from Yakhnev explaining exactly how he'd ended up here.

The prosecution claims that a man in the Dagestan town of Kaspiisk, Ali Magomedov, had found out that two locals were due to transport a large sum of cash to Moscow. He called his friend Arsen Muidov in Moscow, and suggested that they rob the two men during their journey. Muidov recruited Yakhnev into the scheme to give them official cover, and another three men also joined the plot. Late on the night of 26 January 2008, Magomedov spotted the two men leaving, and called Muidov, who set out from Moscow with Yakhnev. The two cars met near the turnoff to Zherdevka, about halfway between Moscow and Dagestan, and agreed they would ambush the third car at a nearby petrol station. When the car approached, they cut off its path, shot at the car a few times, took the money and drove off.

Yakhnev tells it differently. Arsen Muidov was a trusted contact who had worked with him since 1999 and provided many leads.

"In 2007 he [Muidov] introduced me to Ali Magomedov, resident of Kaspiisk, who was in Moscow at the time," writes Yakhnev. "During one of my trips to Dagestan in the summer of 2007 I met with Ali in Makhachkala. I decided to recruit him as an information source. After I became convinced of his loyalty to the federal forces, and the fight against the rebel forces, I started getting him involved."

Magomedov became part of the shadowy network of agents and informers that secret services used to gather information in the north Caucasus, acting as a driver for Yakhnev on occasion and providing information on terrorist plots against the government.

When he met Muidov on 25 January, says Yakhnev, Muidov mentioned Magomedov's tip-off about the money being transferred and asked him to go along with him. Muidov claimed not to know where the money was from or who it belonged to, but asked Yakhnev to help.

"What is happening in the Caucasus is a war," says Samarin, Yakhnev's lawyer. "In a war you have to trust the people you are working with, and Muidov and Magomedov were trusted contacts."

"I decided to go with him because he asked me as a friend," continues Yakhnev. "He didn't tell me what was going to happen, and I don't think he knew himself. One of the reasons for me going was to find out who was transporting this kind of money and with what purpose. It was professional interest."

Nevertheless, it all sounded very suspicious, so Yakhnev left a file on his desk explaining where he was going. He went out drinking with Sergei Badamshin and a couple of other friends, and late the next night, the call came from Magomedov, and so he left Moscow with Muidov and one of the latter's Chechen acquaintances, and began the drive south towards the Caucasus.

He claims that during the incident, he did not even get out of his BMW or know what was happening. Muidov returned with the money and they began to drive towards Moscow. The car was apprehended not long after. The police who stopped the vehicle, terrified when they saw his documents and realised who he was, told him to wait while they radioed Moscow. From somewhere high up, the order came to ignore Yakhnev's right not to be searched and arrest him.

Yakhnev's version of events does sound odd, but it was exactly this sort of illicit money transfer that funded the terrorism that it was his job to prevent. From the rumours I had heard about the corrupt activities of Russia's secret services, it struck me that there were much easier and safer ways for a man in Yakhnev's position who wanted to make money on the side to do so than by driving hours through the night to ambush some unknown Dagestanis.

Yakhnev himself was puzzled by the accusations, says Samarin. "He said to me, 'If I'd wanted to steal the money, it would have been so easy. I would have just showed my papers to any traffic police post; the policemen there would have been obliged to obey my commands, and stop the car, and I could have searched it and walked off with the money without firing a shot.'" When Yakhnev later said that everything would be cleared up if only his employers could produce the report he claims to have written before leaving Moscow, he was told that no such report was found – it had gone missing. He also offered to take a lie-detector test, something that is allowed in some cases with special operatives, but his request was declined.

I asked him what he himself thought was behind his detention.

"Given the fact that I was a high-class specialist in my field, with huge operative abilities and contacts, I was able to talk with the leadership as an equal, and always give my opinion. When everything was OK, they were forced to deal with me being inconvenient, but when this happened, they decided to get their own back, and pretended that this employee never existed. At work, people were told that I had been the boss of a group that carried out contract killings, and had 10 or 20 murders on my hands."

When I tried to make contact with some of Yakhnev's former colleagues, I was told that nobody was willing to talk to me, even anonymously.

"Contact with my former colleagues has been completely cut off," writes Yakhnev. "They were threatened with being fired and put in prison. The DSB [internal security department] got to work on those who were particularly 'eager' to help."

"Acquaintances who enquired in Tambov about getting involved in the case were told to stay away," says Sergei Badamshin. "People have been told in Tambov that if they so much as take an interest in the case, they will meet with the same fate."

***

The courthouse was surrounded by police wielding Kalashnikovs, and riot police in their sky-blue fatigues. One did rounds of the building with a sniffer dog. Inside the small courtroom, eight policemen stood watch, two of them holding automatic weapons. The six accused were led into the courtroom handcuffed, before being padlocked inside a metal barred cage and the handcuffs removed. Yakhnev sat squashed together with the five Caucasians also accused; there was only one other person sitting on the public benches.

The court hearing I attended revolved around a video recording of the interrogation of Magomedov, Yakhnev's contact and also on trial, shortly after he had been arrested. The Dagestani, who appears not to fully understand Russian, is asked about the robbery. The interlocutor, off camera, peppers his sentences with swear words, and tells the Dagestani that he is "100 per cent – no, 1,055 per cent – sure that you have committed other crimes which we"ll find out about," so he better co-operate with this case. The name of Yakhnev is mentioned by the investigator several times, suggesting what he might have been doing, but the Dagestani doesn't admit to anything or implicate Yakhnev. The investigator doesn't ask about any of the others involved.

Strangely, the video is being offered not by the defence as an example of how absurd the investigation was, but by the prosecution as a key piece of evidence. Samarin stands up and argues that, given the video recording was made without prior authorisation, it is inadmissible as evidence anyway. The trial is adjourned for 10 days in order for the defence to prepare a statement to this effect, and the suspects are led out of the courtroom and into a police bus to make the two-hour journey back to the prison in Tambov.

"It's pretty obvious your Yakhnev was set up," says one of the local lawyers defending the other accused, as an aside to Samarin as they all leave the courtroom.

The presiding judge, says Samarin, has so far behaved impeccably, treating the defence arguments with respect and following all due procedures, far more than is common at Moscow courts. At a subsequent hearing, the video evidence was duly disqualified. But nevertheless, he doubts that this will lead to an acquittal.

"You have to remember that in Russia, only 0.8 per cent of cases end in acquittals," he says. Once a case has been brought to court, however weak the evidence may appear, it's as good as over.

***

It's a fact that the Nord Ost siege is one of the most sensitive episodes in recent Russian history, and there are many powerful people who would be anxious to keep a lid on what really happened. So the kind of employee who told the truth about the nature of terrorism in the Caucasus, however useful he was in the field, may well have become regarded as an inconvenience.

In the end, the case throws up far more questions than it answers. It's impossible to know for sure if Andrei Yakhnev is facing jail because of his relationship with Pelevine, because of the things he told her, because of his attempts to stand up against his shadowy masters – or simply because he knew too much. And that, above all, is a dangerous thing in today's Russia.