The Crusades gave the church a militant profile; the Church was responsible for many, many deaths in the Crusades.
The Babylonian Captivity split the leadership of the Church and moved it away from Rome to Avignon in France.
The Great Schism was The East–West Schism 1054, sometimes known as the Great Schism, formally divided medieval Christianity into Eastern (Greek) and Western (Latin) branches, which later became known as the Eastern Orthodox Church and the Roman Catholic Church, respectively.
The Black death affected everyone, not just the Church. The Church, on the other hand, misled their faithful by telling them this was the Judgement of God.