The Crusades were a series of military expeditions sent by various European kingdoms during the Middle Ages. Some atheists (and Muslims) use the Crusades as evidence that Christianity is evil; however, it must be remembered that the Middle East Crusaders only captured territory which was traditionally Christian, and that the Muslims had been conquering various European territories such as Spain, parts of France, Sicily, Egypt, the Levant, Anatolia, among others; massacring or turning into dhimmis the Christian population. Much of this belonged to the Christian Byzantine Empire, whose emperor had to beg help from the Pope. Many massacres occurred, and both sides had their victims; but the Crusaders didn't go to the Middle East "just to kill Muslims", as some would like you to believe.
While it is true that the Crusades were blessed by the Pope and that most Crusaders went fighting for religious purposes, it must be remembered that in the Middle Ages most soldiers thought they were fighting in their god's name, and it was common that the highest religious authority among all the fighters blessed them. Another reason was that Turks had been persecuting Christian pilgrims.
On the other hand, there also occurred the Baltic Crusades, which were for the sole purpose of converting the Pagans of northeastern Europe. Many people were killed for refusing to convert to Christianity. The Baltic Crusades are a true example of the lack of morality in Christianity; but the Middle Eastern Crusades were more a war of defence than anything else.