It is true that in the Ten Commandments we read that it is not permitted to kill. But we do have a duty to protect ourselves and our neighbors in times of war or persecution. The helpless needed to be defended in Palestine and the Holy Sites liberated from oppression.
In 1094 or 1095, Alexios I Komnenos, the Byzantine emperor, sent to the pope, Urban II, and asked for aid from the West against the Seljuq Turks, who taken nearly all of Asia Minor from him. At the Council of Clermont, Urban addressed a great crowd and urged all to go to the aid of the Greeks and to recover Palestine from the rule of the Muslims. The acts of the Council have not been preserved, but we have five accounts of the speech of Urban which were written by men who were present and heard him.
1. Fulcher of Chartres (notes):
"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 meant also for those who are absent."
2. Robert the Monk
From the confines of Jerusalem and the city of Constantinople a horrible tale has gone forth and very frequently has been brought to our ears, namely, that a race from the kingdom of the Persians, an accursed race, a race utterly alienated from God, a generation forsooth which has not directed its heart and has not entrusted its spirit to God, has invaded the lands of those Christians and has depopulated them by the sword, pillage and fire; it has led away a part of the captives into its own country, and a part it has destroyed by cruel tortures; it has either entirely destroyed the churches of God or appropriated them for the rites of its own religion. They destroy the altars, after having defiled them with their uncleanness. They circumcise the Christians, and the blood of the circumcision they either spread upon the altars or pour into the vases of the baptismal font. When they wish to torture people by a base death, they perforate their navels, and dragging forth the extremity of the intestines, bind it to a stake; then with flogging they lead the victim around until the viscera having gushed forth the victim falls prostrate upon the ground. Others they bind to a post and pierce with arrows. Others they compel to extend their necks and then, attacking them with naked swords, attempt to cut through the neck with a single blow. What shall I say of the abominable rape of the women? To speak of it is worse than to be silent. The kingdom of the Greeks is now dismembered by them and deprived of territory so vast in extent that it can not be traversed in a march of two months. On whom therefore is the labor of avenging these wrongs and of recovering this territory incumbent, if not upon you? You, upon whom above other nations God has conferred remarkable glory in arms, great courage, bodily activity, and strength to humble the hairy scalp of those who resist you.
3. The Gesta Version
When now that time was at hand which the Lord Jesus daily points out to His faithful, especially in the Gospel, saying, "If any man would come after me, let him deny himself and take up his cross and follow me," a mighty agitation was carried on throughout all the region of Gaul. (Its tenor was) that if anyone desired to follow the Lord zealously, with a pure heart and mind, and wished faithfully to bear the cross after Him, he would no longer hesitate to take up the way to the Holy Sepulchre.
And so Urban, Pope of the Roman see, with his archbishops, bishops, abbots, and priests, set out as quickly as possible beyond the mountains and began to deliver sermons and to preach eloquently, saying: "Whoever wishes to save his soul should not hesitate humbly to take up the way of the Lord, and if he lacks sufficient money, divine mercy will give him enough." Then the apostolic lord continued, "Brethren, we ought to endure much suffering for the name of Christ - misery, poverty, nakedness, persecution, want, illness, hunger, thirst, and other (ills) of this kind, just as the Lord saith to His disciples: 'Ye must suffer much in My name,' and 'Be not ashamed to confess Me before the faces of men; verily I will give you mouth and wisdom,' and finally, 'Great is your reward in Heaven."' And when this speech had already begun to be noised abroad, little by little, through all the regions and countries of Gaul, the Franks, upon hearing such reports, forthwith caused crosses to be sewed on their right shoulders, saying that they followed with one accord the footsteps of Christ, by which they had been redeemed from the hand of hell.
3. Version of Balderic of Dol
And turning to the bishops, he said, "You, brothers and fellow bishops; you, fellow priests and sharers with us in Christ, make this same announcement through the churches committed to you, and with your whole soul vigorously preach the journey to Jerusalem. When they have confessed the disgrace of their sins, do you, secure in Christ, grant them speedy pardon. Moreover, you who are to go shall have us praying for you; we shall have you fighting for God's people. It is our duty to pray, yours to fight against the Amalekites. With Moses, we shall extend unwearied hands in prayer to Heaven, while you go forth and brandish the sword, like dauntless warriors, against Amalek."
4. Version of Guibert de Nogent
"If in olden times the Maccabees attained to the highest praise of piety because they fought for the ceremonies and the Temple, it is also justly granted you, Christian soldiers, to defend their liberty of your country by armed endeavor. If you, likewise, consider that the abode of the holy apostles and any other saints should be striven for with such effort, why do you refuse to rescue the Cross, the Blood, the Tomb? Why do you refuse to visit them, to spend the price of your lives in rescuing them? You have thus far waged unjust wars, at one time and another; you have brandished mad weapons to your mutual destruction, for no other reason than covetousness and pride, as a result of which you have deserved eternal death and sure damnation. We now hold out to you wars which contain the glorious reward of martyrdom, which will retain that title of praise now and forever."
5. Urban II: Letter of Instruction to the Crusaders, December 1095
Urban, bishop, servant of the servants of God, to all the faithful, both princes and subjects, waiting in Flanders; greeting, apostolic grace, and blessing.
Your brotherhood, we believe, has long since learned from many accounts that a barbaric fury has deplorably afflicted an laid waste the churches of God in the regions of the Orient. More than this, blasphemous to say, it has even grasped in intolerabe servitude its churches and the Holy City of Christ, glorified b His passion and resurrection. Grieving with pious concern at this calamity, we visited the regions of Gaul and devoted ourselves largely to urging the princes of the land and their subjects to free the churches of the East. We solemnly enjoined upon them at the council of Auvergne (the accomplishment of) such an undertaking, as a preparation for the remission of all their sins. And we have constituted our most beloved son, Adhemar, Bishop of Puy, leader of this expedition and undertaking in our stead, so that those who, perchance, may wish to undertake this journey should comply With his commands, as if they were our own, and submit fully to his loosings or bindings, as far as shall seem to belong to such an office. If, moreover, there are any of your people whom God has inspired to this vow, let them know that he (Adhemar) will set out with the aid of God on the day of the Assumption of the Blessed Mary, and that they can then attach themselves to his following. - Pope Urban II's Speech Calling for the First Crusade