Mikhail Khodorkovsky, once his country’s richest man, has resided in “gulag lite,” as he calls the Russian penal system under Vladimir Putin, for six years. Since the spring, on most working days he is roused at 6:45 in the morning, surrounded by guards and packed into an armored van for the drive to court. For two hours each way, the man who once supplied 2 percent of the world’s oil crouches in a steel cage measuring 47 by 31 by 20 inches. Convicted of tax evasion and fraud in 2005, Khodorkovsky now faces a fresh set of charges that add up to the supposed theft of $30 billion. In the dark of the van, Khodorkovsky tries to prepare for his trial, replaying in his mind his night reading, the daily stack of documents from his lawyers. But Russia’s most famous prisoner worries too about what would happen if a car slammed into the van. (Collisions are routine in Moscow’s clotted avenues.) “Your chances of making it out alive,” he wrote me one day this summer, “at any speed, are next to none.”

Khodorkovsky (pronounced ko-door-KOFF-skee) has spent more than 2,200 days behind bars. He cannot receive reporters. Yet the ban has brought a revival of a dissident tradition dating back to Ivan Grozny and Prince Andrey Kurbsky in the 16th century: the epistolary exchange. For several months this year, from July until October, Khodorkovsky and I were able to conduct a series of exchanges — as he has done with other correspondents, both foreign and native — filtered through the hands of lawyers (who transcribe his oral replies) and avoiding the eyes of prison officials. In court, he has maintained that he fails to understand the case against him. The new indictment runs 3,487 pages but boils down to a single accusation: that the former C.E.O. of the Yukos oil firm and his deputy, Platon Lebedev, were part of an “organized criminal group” that stole 350 million tons of oil from their company between 1998 to 2003. The tonnage exceeds Yukos’s production during the period in question. If convicted, Khodorkovsky, whose first sentence ends in 2011, could face an additional 22 years in jail.

In the decade since Putin’s rise, Russians have grown inured to celebrity criminal cases. The murders of politicians, journalists and human rights activists; apartment-house blocks bombed to ruins; the carnage of the hostage sieges in Moscow and Beslan — the acts of horror and terror have numbed the populace. The exception is the delo Khodorkovskogo — the Khodorkovsky case. No other affair has lingered as long in the minds of so many. The case marked a turning point for Russia, the divide between the turbulent Yeltsin years and the stricter rule of the Putin era. And today, in its second iteration unfolding in Moscow, much more than the fate of an oligarch hangs in the balance.

From the start of his presidency on New Year’s Day 2000, Putin was on a roll. But it was the takedown of Khodorkovsky in 2003 that upped the ante. Under Yeltsin, the chieftains of Russia’s vast financial-investment groups held sway over the vital industries (oil, metals, banking and media) and, to a large degree, held the government hostage. That changed on a frigid October night, when masked agents of the Federal Security Service boarded a plane on a Siberian tarmac and enacted one of the most famous perp walks in Russian history, an oligarch returned to the capital at gunpoint.

Khodorkovsky’s arrest stunned Russian nationalists and Western hedge-fund managers alike. Putin had forced the oligarchs to toe a new party line: profits could be blessed, but only if politics stayed off-limits. “The Yukos case marked the start, in 2003, of gosudarstvennoe reiderstvo” — “state raiding” — Khodorkovsky told me in a Russian-language reply last month. For edification, he explained ‘‘reiderstvo,” a word borrowed from Wall Street that has entered the language of Pushkin: “That is, the seizure of others’ property with the aid of state institutions (first and foremost, the organs of law enforcement).” The attacks, he argued from jail, spelled “a disaster for Russian business.” Under Putin, the state blithely acquired a string of Russia’s fattest companies — first and foremost, Khodorkovsky’s own. Despite assurances that the Kremlin would never nationalize Yukos, the state oil company Rosneft, led by Igor Sechin, a Putin confidant and former intelligence officer, soon took over Yukos’s most prodigious fields and refineries.

For Putin, the reclamation project proved a boon. Russia’s titans locked arms in a docile chorus and rushed to finance Kremlin projects. For years, as long as the price of Urals crude soared, Putin could forget about an unruly oligarch in a Siberian prison. He could even decamp from the Kremlin, usher in a handpicked successor (Dmitri Medvedev), move to the prime minister’s office and remain the power behind the throne. But the second Khodorkovsky trial has come at an inopportune time. For a decade, Putinism rested on an unsound social contract, a sacrifice of liberties for stability. Now, however, the global downturn has hit. Russia’s economy is projected to contract by 8 percent in 2009, and the number of Russians below the poverty line has grown to 17 percent. At the same time, the Putin-Medvedev diarchy — diarkhiya, pundits term it — is showing its seams, and the campaign against Khodorkovsky, a cornerstone of Putin’s rule, threatens to open fissures. In Moscow, the circle of those who question the hard line has widened beyond marginalized liberals — to oligarchs, politicians, even journalists, who once marched in lock step with the Kremlin. Their voices are unlikely to spur a groundswell of support for Khodorkovsky, much less an organized political opposition. But they do pose a discomfiting question, one that has hung over the Kremlin since the legal campaign began: Who fears a free Khodorkovsky?

Read the full version of the article in the New York Times Magazine.