The Crusades had two immediate causes. The first was the attacks by Muslims upon pilgrims going to Jerusalem, and destruction of the shrines there. The second, equally important was an appeal for help from the Eastern Christians who were suffering a renewed Islamic invasion by the Seljuk Turks. In 1095 Pope Urban the Second called for Christians to unite in a Crusade.
From Pope Urban II’s call at the Council of Clermont in 1095
Freshly quickened by the divine correction, you must apply the strength of your righteousness to another matter which concerns you as well as God. For your brethren who live in the east are in urgent need of your help, and you must hasten to give them the aid which has often been promised them. For, as the most of you have heard, the Turks and Arabs have attacked them and have conquered the territory of Romania [the Greek empire] as far west as the shore of the Mediterranean and the Hellespont, which is called the Arm of St. George. They have occupied more and more of the lands of those Christians, and have overcome them in seven battles. They have killed and captured many, and have destroyed the churches and devastated the empire. If you permit them to continue thus for awhile with impurity, the faithful of God will be much more widely attacked by them. On this account I, or rather the Lord, beseech you as Christ’s heralds to publish this everywhere and to persuade all people of whatever rank, foot-soldiers and knights, poor and rich, to carry aid promptly to those Christians and to destroy that vile race from the lands of our friends. I say this to those who are present, it is meant also for those who are absent. Moreover, Christ commands it.
So were the Eastern Christians really in mortal Danger?
The answer is yes. A new wave of conquest had been launched by the Seljuk Turks, who would give their name to the land now called Turkey.
This is from a contemporary account of their attack on Christian Armenia in 1059, 30 years before the Crusades.
On Sunday 6th August the siege of Sebastea began, as did the slaughter; thousands of corpses littered the ground. What a dreadful scene. The bodies of highly renowned men were piled in a heap as if a forest of trees had been felled. and the ground was soaked with blood…
They ruthlessly massacred an immense number of people, carried off booty and took untold numbers of captives, men and women, young boys and girls, whom they sold into slavery… Fateful day! In a matter of minutes Sebastea and the surrounding plain were bathed in blood. The clear waters of the River Kizil Irmak which cuts through the city walls, suddenly flowed red.
In 1064 the Turks returned. He made his way towards Armenia and entered the country; the inhabitants were put to the sword and driven into slavery. The infidels were so numerous that they covered the plains and closed off al the escape routes. Then he invaded Georgia, bringing death and slavery wherever he went. … The Turks exterminated all the inhabitants, men, women, priests, monks and nobles; the young boys and girls were taken away captive into Persia.."
Chronicle of Matthew of Edessa.
I would say the Crusades were clearly a Just war in that they were basically defensive. A strike back against 600 years of Muslim aggression and conquest. Many modern historians have tried to turn this upside down and present the Crusades as blatant Christian aggression. That is false.