Hans-Dietrich Genscher, right, of the liberal Free Democratic Party, welcomes Mikhail Khodorkovsky at Berlin's Schonefeld airport on Dec. 20. (HANDOUT/Reuters)

As his country’s most famous political prisoner, Mikhail Khodorkovsky spent many days over the past decade being shuttled from one penal colony to another on Russia’s slow, creaking trains. But in a dramatic change in his fortunes, the former oil tycoon found himself on a private jet bound for Germany on Friday after being granted a pardon by Russian President Vladimir Putin.

Events have moved quickly since the unexpected announcement a day earlier that Khodorkovsky would be allowed to walk free. But a mystery remained about what led to his release and what his plans for the future are.

Khodorkovsky, who was jailed in 2003 on charges of tax evasion and fraud that his supporters say were politically motivated, had served a long term and his mother was ill, the Russian president said.

True to his word, Putin inked a decree Friday pardoning Khodorkovsky and ordering the immediate release of one of the president’s most vocal critics.

No reporters were present to witness Khodorkovsky’s departure from a penal colony in northwest Russia that was once part of the network of gulags the Soviets installed close to the Arctic Circle.

Russia’s penitentiary service said Khodorkovsky was on his way to Berlin, where his mother was undergoing medical treatment. But there was some confusion after Russian reporters discovered that Marina Khodorkovsky was still in Moscow and had received no news from her son.

Later in the day, the German Foreign Ministry confirmed that he had landed at Berlin’s Schöne­feld Airport, where he was greeted by a ministry representative. Der Spiegel reported that Khodorkovsky had been met by the former German foreign minister, Hans-Dietrich Genscher, who had helped organize the charter flight.

Despite all the muddle, it appears that plans to release Khodorkovsky had been in the works for some time. In a statement late Friday, Khodorkovsky said he had appealed to Putin for a pardon for “family reasons” on Nov. 12. But his former business partner Platon Lebedev, who has also been in jail for 10 years, chose the same moment to issue a statement through his lawyers saying he would not be seeking a pardon for now.

In a chilling tale, the Kommersant business daily reported that Russian secret service officers had visited Khodorkovsky in jail some weeks ago to outline his bleak prospects. No lawyers were present at the meeting.

Khodorkovsky was hoping to be released next year in August when his two concurrent sentences expire. However, his visitors bore alarming news that state prosecutors were preparing a third case that could keep him in jail for several more years. The deteriorating health of Khodorkovsky’s mother was also discussed.

Although unconfirmed, the Kommersant report suggests that Khodorkovsky came under pressure to strike a deal with authorities to secure his release.

If that was the case, it appears that the parties had not agreed on a crucial detail. Khodorkovsky stressed in his statement that while appealing to Putin for a pardon he had not confessed his guilt. That assertion contradicted earlier statements by several Russian officials that a request for a pardon was tantamount to an admission of wrongdoing.

“His amnesty request to the president has been submitted. If he is asking to be pardoned, this means he is admitting guilt,” Dmitry Peskov, a spokesman for Putin, told the Interfax news agency on Thursday.

After Khodorkovsky was arrested in 2003, his Yukos oil corporation came under sustained attack from Russian tax collectors and was eventually sold off at bankruptcy auctions. The state oil company, Rosneft, scooped up most of Yukos’s best assets at the sales.

Khodorkovsky was forced to give up his Yukos holdings, but other groups of shareholders are suing the Russian government and Rosneft in international courts for billions of dollars for expropriating their assets.

The powerful president of Rosneft, Igor Sechin, said Friday that Khodorkovsky’s appeal for a pardon improved the “legal grounds” to protect Rosneft’s interests in the Yukos case, although it was not clear how this might come about.

Sechin also offered a somewhat implausible solution to the problem of what Khodorkovsky might do next, saying he would consider him for a job at Rosneft if an appropriate position came up.

Lyudmila Alexeyeva, the head of the Moscow Helsinki Group — Russia’s oldest human rights organization — saw a different outcome: Khodorkovsky would become a much needed “spiritual leader” in Russia, filling a role similar to those played by Mohandas K. Gandhi in India and Vaclav Havel in the Czech Republic. “He will become one of us. I am sure we will cooperate. I am ready to do everything I can to help him,” she said.