Each side was organized in separate factions; the Catholics in the Holy League and the Protestants in the Evangelical Union. The spark that ignited the explosion came when the Archbishop of Prague ordered the destruction of a Protestant church. When the king ignored the protests and appeals from the masses, in a typical Bohemian custom of throwing renegade officials out of a window, the people seized two of the kings royal governors, and threw them out of a palace window. Civil war ensued and spread throughout Europe. The Bohemian Protestants deposed Catholic king Ferdinand and chose Protestant Frederick. In a twist of fate, the ousted king Ferdinand later became Holy Roman Emperor which gave him the necessary power to crush the Bohemian Protestants.

After Bohemia was soundly defeated, other Protestant countries feared that Catholics, aided by Ferdinand might try to destroy Protestantism altogether. Protestant Danish king Christian IV attacked the Emperor, but were defeated over and over. The Treaty of Lubeck with the Edict of Restitution gave much Protestant church property back to Catholics, and this created a new source of friction in Germany.

Fearing Catholic resurgence and especially political domination from Ferdinand, the Swedish king Gustavus Adolphus entered the war and successfully defeated the Catholic armies. Tragically, both leaders were killed in battle, Protestant Adolphus and Catholic Tilly.

The war now lost its religious character and became a political struggle as French Cardinal Richelieu (Catholic) entered the foray on the side of the Protestants because he also wanted to thwart the Hapsburg family from dominating Europe. Truly politics does create uncommon bedfellows. It was Richelieu who mercilessly persecuted French Protestant Huguenots resulting in the emigration of perhaps 800,000 people from France. Now he was fighting with Protestants. The superior French generals united with the Swedish army defeated a battle weary Catholic Hapsburg force, but in a prolonged series of engagements with no single, decisive battle victory.

It took four years to reach a peaceful agreement. Protestant and Catholic representatives met in separate cities of the German district of Westphalia and negotiated a settlement that gave certain lands to the French or Swedish, and finally recognized the Calvinists. The effects of the different wars had a terrible outcome, especially for Germany. Thousands of civilians were killed, whole villages and farms were decimated, and survivors had little resources with which to rebuild. Many people left for America to start over. Historians conservatively estimate that it took more than a century for Germany to finally get back on its feet.

Protestants and Catholics had failed to exterminate each other, and were forced into mutual toleration by such factors as battle weary exhausted armies, political despair, and the humility of defeat. It also reminded both sides that worship is a freedom given by God that man should not attempt to control. Historians point out that if only Pope Leo X had been more interested in religion and domestic peace instead of artwork, there may not have been a Reformation. Likewise, if Charles V had been more interested in people than his borders, tens of thousands would not have died in European wars during his and future generations. All too often history demonstrates that wickedness enjoys its finest hour in the hearts of kings.