From behind bars, the oligarch who was once Russia's richest man, has challenged the Russian Prime Minister to answer in court a series of questions which he has supplied exclusively to The Independent. Lawyers for Mr Khodorkovsky, who has been in prison since his arrest in 2003 and subsequent conviction for fraud, intend to call the former president, still regarded as the most powerful man in Russia, as a witness when the defence questioning in Mr Khodorkovsky's latest trial opens, probably later this month.
The jailed businessman claims that the prosecution case is full of flaws and contradictions, and challenges Mr Putin to explain his actions and statements relating to Rosneft, the oil company that became Russia's biggest after Mr Khodorkovsky's downfall.
"Your prosecutors claim that I ran Yukos not as an official chairman, but as the leader of an organised criminal group," Mr Khodorkovsky writes, addressing Mr Putin directly. "When you discussed Yukos's problems with me, with whom did you think you were talking?"
After Mr Khodorkovsky's arrest and imprisonment, Rosneft purchased major Yukos assets at state-run auctions. It is chaired by Igor Sechin, a Kremlin insider and a close associate of Mr Putin. "Why is it that Rosneft paid exactly the same per tonne of production, but your tax authorities have no complaints about Rosneft?" Mr Khodorkovsky asks the Russian Prime Minister.
Mr Khodorkovsky was given a nine-year jail sentence in 2005, later reduced to eight, and had been serving it in a remote Siberian prison six time zones away from Moscow. However, a year ago, he was brought to the capital to stand trial on new charges of embezzlement and fraud. If he is found guilty, he could be imprisoned for another two decades.
In written answers to questions put to him by The Independent through his lawyers, Mr Khodorkovsky also reflected on the liberal rhetoric of Mr Putin's anointed successor, Dmitry Medvedev, as well as on his own state of mind given that he may well spend much of the rest of his life behind bars.
Most days, he and co-defendant Platon Lebedev are driven from the notorious Matrosskaya Tishina prison to the central Moscow courtroom where the trial takes place. The small band of supporters, liberal journalists and well-wishers that attend each day often collapse into giggles as the prosecuting lawyers tie themselves into knots with the reams of court documents.
Both Mr Khodorkovsky and Mr Lebedev have been active participants in the courtroom, sitting in the glass cage that has been nicknamed the "aquarium", passing documents back and forward to their lawyers through a small window, and frequently questioning the prosecution witnesses themselves.
Nearly a year in, the defence team believes that the prosecution is finally about to finish putting its side of the argument, and in the next two weeks expect to begin calling their own witnesses to the stand.
Mr Medvedev, since coming to the presidency in 2008, has often struck a very different tone to his predecessor. He has spoken openly about the scale of corruption in Russia, and professed a desire to end the climate of "legal nihilism" in the country.
But many analysts claim that Mr Medvedev is simply one half of a "good cop, bad cop" act with Mr Putin, and that while he has made a few cosmetic changes, his words mean little. There is a suggestion that he is keeping the seat warm for a potential return to the presidency by Mr Putin in 2012. It is doubtful whether he could give the order to free Mr Khodorkovsky, even if he wanted to.
Mr Khodorkovsky said that he believes Mr Medvedev's liberal inclinations to be genuine. "As far as I understand, Medvedev has a sincere and strong desire to change the most odious manifestations of the current political system – corruption and the ineffective system of law enforcement and court proceedings," writes the imprisoned former oligarch. "But reasonably soon, the President's actions will bring him to a boundary, after which specific changes will not be possible without modernising the political system as a whole. And of course it's a big question whether Dmitry Medvedev can see this through."
Even some usually loyal government figures have decried the second set of charges against Mr Khodorkovsky as absurd, but in recent months, when asked about the Khodorkovsky case, Mr Putin has become even more aggressive. On a recent trip to France, the Russian Prime Minister compared him to Al Capone, and during a televised phone-in with the nation, accused Mr Khodorkovsky of organising several murders, a crime for which he has never been charged.
It is widely believed that Mr Khodorkovsky's troubles began when he reneged on an unwritten agreement between the Kremlin and the oligarchs made soon after Mr Putin's accession to the Kremlin in 2000. The small clique of businessmen who had grown extremely rich in the 1990s were allegedly allowed to keep their wealth without question as long as they stayed out of politics. Recently released memoirs of Lord Browne, the former chief of BP, shed some rare light onto the duel between Mr Khodorkovsky and Mr Putin. Lord Browne claims that when he invited the Yukos chief for lunch at his Cambridge home prior to his arrest, the oligarch spoke about "getting people elected to the Duma, about how he could make sure oil companies did not pay much tax, and about how he had many influential people under his control. For me, he seemed too powerful." Later, writes Lord Browne, Mr Putin told him, "I have eaten more dirt than I need to from that man", referring to Mr Khodorkovsky.
Rumours after the accession of Mr Medvedev to the Kremlin suggested that a deal was discussed whereby Mr Khodorkovsky would be released in return for leaving Russia or staying out of politics, but the former oligarch strongly denies this in his interview with The Independent. "I have never been offered any kind of deal, neither during the first case, nor at the current time," he writes.
"I understand perfectly well that there are several bureaucrats who initiated the second trial and who want me behind bars forever. But whatever happens, I am going to defend my position and my innocence. Firstly, I don't think the outcome of the case is preordained. And secondly, I don't want to allow anyone the possibility to think that I am guilty of something. So I'm going to prove that I am in the right so comprehensively that nobody will have any room left for doubt."
Whether that will be enough to earn his acquittal is doubtful. Political analyst Dmitry Oreshkin says the system, and Mr Putin, work by "Stalinist, bandit logic", whereby releasing Mr Khodorkovsky would be seen as a sign of weakness, not of compassion. There is also a worry that Mr Khodorkovsky could become a figurehead for opposition forces. Few Russians have much time for the oligarchs, who they see as plundering the country's resources during the chaotic 1990s while millions were scraping by below the poverty line. But Mr Khodorkovsky's time in prison may have given him a moral legitimacy that other businessmen lack.
Perhaps partly because of this, few analysts believe there is a real chance of him being found not guilty, which means years, if not decades, of prison life beckon. "Of course, like any normal person, this doesn't make me feel happy. I want to be free, to live with my family and help my country," Mr Khodorkovsky said when asked in the interview if he was psychologically prepared to spend the next two decades behind bars. "But in any case, I don't plan to despair and give up hope".
Khodorkovsky defence: Questions for the Prime Minister
Mr Khodorkovsky says he wants to ask the Russian premier the following:
* Your prosecutors claim I ran Yukos not as an official chairman, but as the leader of an organised criminal group. When you discussed Yukos's problems with me, with whom did you think you were talking?
* Your prosecutors accuse me of stealing Yukos' production from 1998 to 2003. When you, in 2003, personally congratulated Yukos for its successes in commercial and social activities, is this what you were referring to?
* When you announced to the country in February 2003 that Yukos had no problems with the tax authorities, and that everything had been regulated, what taxes were you talking about, given that your prosecutors say that all the oil had been stolen?
* Your prosecutors say I stole Yukos's oil, while your representatives in Strasbourg [Yukos is suing Russia at the European Court of Human Rights] say Yukos sold its oil, but did not pay enough tax. Which is lying? Why is it Rosneft paid the same per tonne of production, but your tax authorities have no complaints about Rosneft?
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