Only one year earlier, in the summer of 1098, the (Muslim) Fatimid Emir (commander) al-Afdal Shahinshah had taken Jerusalem from the (also Muslim) Seljuk Turks after a 40-day siege, on orders of the Fatimid Vizier (Minister of State) al-Musta’li, ruler of Egypt. Many months of political and diplomatic maneuvering with the Franj (Franks–the Arabic term used for all Western European Crusaders) and the Rumi (Romans–actually the Greeks of the Byzantine Empire) had not gotten the vizier the concessions he wanted, so he simply had sent Emir al-Afdal to seize the city the Crusaders were coming to capture, thereby presenting the Franj invaders with a fait accompli.
These 1098 events indicate that the negotiations between the Byzantine and Franj on the one hand, and the Muslim Fatimid rulers of Egypts on the other hand on combined efforts against their common enemy, the Muslim Seljuk Turcs that controlled the eastern part of the Byzantine Empire as well as Jerusalem, had turned sour.
These negotiations may have been one of the reasons why the Crusader army, after the successful siege of Antioch in June 1098, remained in that area for the rest of the year. Other reasons being disagreement between the leaders of the army on what to do next. Bohemond of Taranto had claimed Antioch for himself and wanted to remain there. Baldwin of Boulogne remained in Edessa, captured earlier in 1098. By the end of the year 1098, the minor knights and infantry were threatening to march to Jerusalem without their leaders. Eventually, on January 13, 1099 Raymond of Toulouse began the march south, down the coast of the Mediterranean, followed by Robert of Normandy and Bohemond's nephew Tancred, who agreed to become his vassals.
The 1099 siege and conquest of Jerusalem is notable for the mass slaughter of Muslim and Jewish perpetrated by the Christian crusaders, which contemporaneous sources suggest was savage and widespread. Atrocities committed against the inhabitants of cities taken by storm after a siege were normal in ancient and medieval warfare by both Christians and Muslims. The Crusaders had already done so at Antioch, and Fatimids had done so themselves at Taormina, at Rometta, and at Tyre. However, the massacre of the inhabitants of Jerusalem may have exceeded even these standards. Historian Michael Hull has suggested this was a matter of deliberate policy rather than simple bloodlust, to remove the "contamination of pagan superstition" (quoting Fulcher of Chartres) and to reform Jerusalem as a strictly Christian city.
Sources text historynet.com and Wikipedia. Illustration a 13th-century miniature depicting the siege, Wikipedia