On November 27, 1095, near Clermont, France, Pope Urban II called for the First Crusade. Note that this was the first crusade -- there had never been anything like it in the history of Christendom. People didn't know what it was. Urban wanted, it seems, an organized trip to Palestine, where the Christians would fight the Moslems and take back the holy sites from the infidels; of particular concern was Jesus' grave. However, it soon got out of hand. Organized armies of Crusaders there were; they did what Urban wanted, capturing Palestine and making it into a Christian state for many decades. But separately were various unruly bands of Crusaders. It is these latter with which we are primarily concerned.
The major such band was lead by someone called Peter the Hermit. He went through France after Urban's call, building up his band of people, and later, in the spring of 1096, moved toward Germany. The Jews of France were worried from the start. They realized what a Crusade could mean for them, and they sent a message to the Jews of the Rhineland (Germany), asking the latter to pray for them. The German Jews, though, were unconcerned. They were thus taken by surprise as the events of the spring unfolded.
The French Jews, concerned perhaps for their own welfare, perhaps for the German Jews', gave Peter a letter of introduction to the German Jews, asking the latter to help him financially; this they (specifically, the Jews of Trier) did, and Peter's band itself did little damage to the Jews at all. It was the other unofficial bands of Crusaders, especially that of one Count Emicho, who, coupled with the local burghers, inflicted the most damage:
As the crusading host, often no better than a mob, gathered, any Jewish community on its line of march was in jeopardy. The Bishop of Speyer stopped the rioting quickly by using force. . . . The Archbishop of Cologne did the same. But at Mainz the Archbishop had to flee for his own life. The Jews tried to fight but were overcome. . . . The ancient, rich and populous Jewish communities of the Rhineland were destroyed, most Jews being killed or dragged to the fonts.
-- Johnson, page 208.
Most of those who remained fled eastward, and the great Jewish communities of the Rhineland were great no longer. Indeed, of all the major teachers of Torah in the area, only one, Rabbi Yitzchak (son of Asher), survived the First Crusade; the decline of the German seminaries followed soon after (Agus, "Rashi", p. 248).