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His conflict with the Ottoman Turks was the final cause of his undoing.
Unwilling to compromise with the Turks, and stubbornly determined that he could unify all of Christendom with a new Crusade, he started a long and indecisive war with the Turks in 1593.
This war lasted till 1606, and was known as " The Long War ".
By 1604 his Hungarian subjects were exhausted by the war and revolted, led by Stephen Bocskay.
In 1605 Rudolf was forced by his other family members to cede control of Hungarian affairs to his younger brother Archduke Matthias.
Matthias by 1606 forged a difficult peace with the Hungarian rebels ( Peace of Vienna ) and the Turks ( Peace of Zsitvatorok ).
Rudolf was angry with his brother's concessions, which he saw as giving away too much in order to further Matthias ' hold on power.
So Rudolf prepared to start a new war with the Turks.
But Matthias rallied support from the disaffected Hungarians and forced Rudolf to give up the crowns of Hungary, Austria, and Moravia to him.
Matthias imprisoned Georg Keglević who was the Commander-in-chief, General, Vice-Ban of Croatia, Slavonia and Dalmatia and since 1602 Baron in Transylvania, but soon left him free again.
At that time the Principality of Transylvania was a fully autonomous, but only semi-independent state under the nominal suzerainty of the Ottoman Empire, where it was the time of the Sultanate of Women.
At the same time, seeing a moment of royal weakness, Bohemian Protestants demanded greater religious liberty, which Rudolf granted in the Letter of Majesty in 1609.
However the Bohemians continued to press for further freedoms and Rudolf used his army to repress them.
The Bohemian Protestants appealed to Matthias for help, whose army then held Rudolf prisoner in his castle in Prague, until 1611, when Rudolf was forced to cede the crown of Bohemia to his brother.

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