When you think of the Crusades you would most likely assume the war fought between Christian and Muslim forces for control of the Holy Land, however the Northern Crusades were a different story altogether.
In 1193, Pope Celestine III declared a crusade to eliminate the Pagan's from northern Europe (in particular the Baltic states), which was driven by the northern Christian kingdoms. Even though this conflict was based on religion, the northern Saxon and Danish armies had been at war with the Baltic states for centuries.
One of the preceding events in the conflict was that of the Wendish crusade, a conversion war against the Polabian state. It was predominantly fought by the Swedish and Danes against the Slavs, and eventually handed Wagria and Polavia to the Germans, despite the limited success in converting the Slavs to Christianity in the beginning.
By the start of the 12th century, the Baltic regions (modern day Estonia, Latvia and Lithuania), had entrenched themselves and their Pagan beliefs, creating a divide between the two major Christian states, the western Roman Catholics and the Eastern Orthodox. Estonia in particular was attacked often by both states, and at times had war waged upon them by the northern Christian kingdoms of Sweden and Denmark. Estonia fought back at times against the Swedes and Danes, in a time known as the Livonian Crusades.
When the northern German Christian provinces were strong enough to enter the campaign in the early 13th Century, they commenced a decades long battle for control of Estonia, which eventually fell in the Germans favour. The Danes and Swedes also attacked Estonia from the coast, and despite Estonia's long resistance, northern Estonia eventually became Danish controlled territory.
At the same time, the province of Masovia (modern day north-Eastern Poland) began a campaign to take the pagan controlled Prussia, which they had attempted to take many times over the years with no success. This time however they were aided by the Teutonic Knights (an order of German crusading Knights). The Teutonic order was originally created to protect Christian pilgrimages to the holy land.
Once the knights had gained control of Prussia, they set their sights on pagan Lithuania. The Lithuanians took measures to stop the attacks including the baptism of the king, but this didn’t stop them. The knights couldn’t make any head way in Lithuania, and a century later Lithuania became a Christian convert when the Lithuanian Grand Duke married the Queen of Poland. This still didn’t stop the knights who wanted control of the Baltic region, and battles continues to rage for a few more decades until the Lithuanians finally defeated the knights with the help of Poland, Moldova and the Czechs.
Various battles continued to rage over the next century, and by the time the crusade was done, paganism was virtually eliminated from northern Europe, by force and by conversion.