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A member of a Pro-Russian self-defense force takes down a Ukrainian Navy flag, left, as the other raises the Russian flag at the Ukrainian Navy headquarters in Sevastopol, Crimea, Wednesday, March 19, 2014. An Associated Press photographer said several hundred militiamen took down the gate and made their way onto the base. They then raised the Russian flag in the square by the headquarters. The unarmed militia waited for an hour on the square before the move to storm the headquarters. Following the arrival of the commander of the Russian Black Sea fleet, the Crimeans took over the building.Andrew Lubimov/The Associated Press

The Ukraine government's tenuous hold on Crimea all but ended Wednesday as military bases were overrun by pro-Russian forces and the head of the Ukrainian navy was held for questioning by Crimean officials.

Kiev's powerlessness was illustrated early in the day when acting Prime Minister Arseniy Yatsenyuk dispatched his defence minister to Crimea to negotiate free passage for Ukrainian soldiers, only to have his plane turned back by Crimean authorities as they sent in troops to take over bases.

By evening, Russian flags flew at three military compounds, including the Ukrainian navy headquarters, where the commander was detained. Pictures of dejected soldiers walking out with suitcases and bags filled Ukrainian television screens.

All the government in Kiev could do was set up a support line for people leaving Crimea and organize plans to evacuate troops across the border. Officials did make a few other token gestures, such as pulling out of the Commonwealth of Independent States, a loose collection of 11 former Soviet republics, and introducing visas for Russian visitors. The country's security chief also asked the United Nations to declare Crimea a "demilitarized zone."

At one point the country's acting President, Oleksandr Turchynov, issued an ultimatum, warning the Russians of consequences if the naval commander was not released by 9 p.m. local time. The deadline came and went with no word on the commander's whereabouts. In the end it was Russia's Defence Minister, Sergei Shoigu, who asked the Crimean leaders to release the commander "and not to prevent his departure for Ukraine," according to a ministry statement.

Outside Ukraine, the United States voiced its concern over Russia's actions but President Barack Obama ruled out military intervention. "We are not going to be getting into a military excursion in Ukraine," he told a San Diego television station. "There is a better path, but I think even the Ukrainians would acknowledge that for us to engage Russia militarily would not be appropriate and would not be good for Ukraine either," Mr. Obama added.

Anders Fogh Rasmussen, the secretary-general of NATO, was more blunt. Russia's move to annex Crimea has triggered "the gravest threat to European security and stability since the end of the Cold War," he told a gathering at a Washington think tank. His concern, he added, is "that this won't stop … I see Crimea as an element in a greater pattern, in a more long-term Russian, or at least Putin, strategy."

United Nations Secretary General Ban Ki-moon was scheduled to land in Moscow on Thursday, where he will meet with Russian Foreign Minister Sergei Lavrov. Russian state media reported that Mr. Ban "may" also meet with President Vladimir Putin before flying to Kiev on Friday, the day before Prime Minister Stephen Harper is due in the Ukrainian capital.

The Russian leadership is expected to stick to its key points in meeting Mr. Ban – that the referendum in Crimea, and its subsequent annexation to the Russian Federation, is legal.

Moscow also argues the crisis in the region has been caused not by its actions, but by the instability in Kiev following the change of power there, which it claims was a Western-sponsored coup. Mr. Lavrov has presented the U.S. with a five-point proposal calling for international recognition of the Crimean vote, a national unity government in Kiev and a new Ukrainian constitution that gives more autonomy to regions and makes Russian an official second language. The proposal also says Ukraine must have a "neutral military and political status."

Gleb Pavlovsky, a former adviser to Mr. Putin, said the Kremlin views those demands as essential to de-escalating the situation, and that Russia is sending the West a message that it won't tolerate a Ukraine that's a member of the European Union or NATO.

"Putin has been improvising, like a jazz musician. He didn't know himself how far he would go," Mr. Pavlovsky said in an interview. He added: "The integration of Crimea into Russia is the most serious signal that Europe and the West need to stop the crisis. How far this will go is not up to only Putin. It [also] up to the situation in Ukraine, and the signals that the U.S. and Europe give to Kiev."

The Kremlin on Wednesday hinted it could retaliate in asymmetrical ways if the West pressed ahead with economic sanction against the Russian leadership over Ukraine. Deputy Foreign Minister Sergei Ryabkov told the Interfax news agency that Russia didn't want to use negotiations over Iran's nuclear program as a bargaining chip in its showdown with the West, but might have to do so in response to steps taken by the U.S. and EU.

With a report from Reuters

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