It has been a battle for power over Russia's riches and its futures. In the far away West, Khodorkovsky and others successful industrialist like him are looked up and perceived as the guys in the white hats, modern liberals committed to free-market ideals. No matter how questionable the means and circumstances were in which they accumulated this wealth, they have now cleaned themselves and are working for the virtues of shareholder rights, transparency and corporate governance. Now oligarchs such as Khodorkovsky were ready to cut deals with the best in the West. Ranged against these oligarchs, in the "black hats," were the reactionary political forces (Lead by Past president and now prime minister-Putin) that were and are against the West. These are Russian nationalists who favour the preservation of their past ideologies over the National economic interest.
The re-arrest of Khodorkovsky ultimately points to the weakness of Putin's rule: Putin has not denied from the possibilities of contesting 2012 president elections. Putin, like a master Russian chess player has been brilliant at negotiating between different factions, playing them off, against one another. But this mark a watershed, Putin has taken the most dramatic action possible against the leading oligarch (The way he has intervened the legal proceedings).
Putin has pushed fragile Russian economy back by numerous years as this will badly hurt sentiments of the future FDI investors.