As he bedded down for a sixth night in a Moscow jail, the 40-year-old billionaire was likely to be counting the warning shots he ignored and pondering the capriciousness of a system he looks to have badly underestimated.
Being snatched unceremoniously from a plane on Saturday and charged with tax evasion and fraud may yet prove to be only the beginning of a long hard road for the suave oil tycoon.
He learned on Thursday, possibly from the television in his five-by-four metre cell, that the huge stake worth billions of dollars he holds in his company YUKOS had been blocked by the state.
And many observers of the Russian scene expected further moves in coming days against YUKOS - with nothing on the horizon to suggest Khodorkovsky will be spared the full weight of Russian justice.
Cut and run
Khodorkovsky, who has time and again chanced his arm by raising the political stakes in his stand-off with the Kremlin, once said he would prefer to be a political prisoner than a political emigre.
"Never pull out a gun unless you intend to shoot"
President Vladimir Putin
But he may now be ruefully comparing his fate to two other Russian moguls who made their fortunes in the 1990s - Boris Berezovsky and Vladimir Gusinsky - and who cut and run to live in the West.
Though exiles now, both at least have some of their wealth - and above all their liberty.
Time and again, the dapper Khodorkovsky - either through principle, bravado or lack of judgment - chose to ignore the unmistakable signs that the Kremlin was losing patience over his thinly veiled political ambitions.
He also may have underestimated the hard edge to President Vladimir Putin who once said the KGB, the state security force he served as a foreign intelligence spy, had taught him one good lesson: "Never pull out a gun unless you intend to shoot."
Putin made clear on Monday he had washed his hands of Khodorkovsky's fate, saying his case was a matter for the courts.
The last missed signal for Khodorkovsky came on October 21 when Russia's deputy prosecutor general observed prophetically: "Personally, I would not like to see Khodorkovsky or anyone else sitting behind bars ... but boys, stop cheating, stop stealing."
Four days later Khodorkovsky was behind bars. Did he assume his vast wealth and the help of moderates in the Kremlin would protect him from Russian justice?
Did he assume his friends in the US business and political elite with whom he rubbed shoulders would give him cover?
The first real warning shot to Khodorkovsky came in July when major YUKOS shareholder Platon Lebedev, a close ally, was arrested on theft charges going back to a 1994 privatisation deal.
Khodorkovsky immediately announced he had no intention of yielding to pressure and fleeing the country.
He went later in the month to an economic conference in Idaho, raising speculation he would stay in the United States.
But he returned saying: "Today we must definitely decide if our country's future will be totalitarian. If we hold strong, this will be resolved once and for all."
Matrosskaya Tishina prison in
Moscow is home for the tycoon
Nor did Khodorkovsky react when Putin remarked during one of their Kremlin meetings: "YUKOS has excessive resources but how they got them is a matter for discussion."
Searches of YUKOS premises followed Lebedev's arrest and then prosecutors charged another major YUKOS shareholder Vasily Shakhnovsky - but still Khodorkovsky refused to lower his public profile.
"It's the rock star syndrome. He made his wealth so quickly he lost contact with reality," said the chief executive of a top investment bank on Thursday.