On April 2, 2002, a routine arrest raid in Bethlehem quickly spiraled into one of the most unexpected controversies resulting from an Israeli military operation in the past decade. Fleeing IDF troops, some 220 men and teenagers, among them dozens of armed Palestinian terrorists, took refuge in the city’s Church of the Nativity, which is said to be the birthplace of Jesus Christ.

Palestinian terrorists had sought refuge in the church’s Manger Square a number of times during previous raids and had used the area to stage operations against Israelis on the outskirts of Bethlehem and Jerusalem. The Palestinians believed that Israeli forces would not enter the square. When IDF troops advanced on the square, they entered the church, under the correct assumption that soldiers would not follow them inside.

The IDF was aware of the possibility that militants might flee into the revered sanctuary and had a plan to prevent it. A special forces unit was to be flown by helicopter to the entrance of the church to block anyone from entering it during the routine raid. The troops, however, arrived late and dozens of Palestinian militants and civilians made it inside the site.

The siege on the Church of the Nativity took place toward the beginning of Operation Defensive Shield, a widespread counter-terrorism operation to retake many Palestinian cities in the West Bank following a wave of deadly suicide bombings and terrorist attacks. The events in Bethlehem also coincided with the start of a siege on the Jenin Refugee Camp. Both incidents drew international condemnation at the time.

Neither side expected the siege to ever take place and certainly not to stretch on over five weeks. The two sides also did not anticipate the complications of brokering the surrender of terrorists holed up in one of the world’s holiest buildings. Nonetheless, the IDF quickly dispatched professional negotiating teams to broker the Palestinians’ surrender. PLO Chairman Yasser Arafat sent a number of teams to negotiate with Israel; even the CIA and other Western powers played a role in the talks.

For weeks, the Palestinians refused to budge on their refusal to accept either surrender or exile for the fighters laid up in the church.

Light clashes took place regularly between the Palestinian terrorists inside the church and Israeli troops surrounding it. IDF snipers took aim at any terrorists who dared reveal themselves in windows or on the perimeter of the church. A number of Palestinians, a monk and two Israeli Border Police officers were wounded in the short, sporadic firefights.

During one incident, in an attempt to locate the source of nighttime gunfire from the church, the IDF fired a flare into the air, which set fire to a room in the holy site. A Palestinian militant who rushed to extinguish the fire was shot dead by an Israeli sniper. As violent incidents continued in and around the church, international pressure to end it mounted.

Ultimately, Yasser Arafat ordered his negotiating teams to accept most of Israel’s conditions for ending the siege: the exile of a number of terrorists to European countries and others to the Gaza Strip. Those negotiations were scuttled a number of times. At one point, a deal was reached to exile some of the terrorists to Italy but nobody had bothered to consult with Rome.

Another contentious point in the negotiations was what to do with the weapons Palestinians had brought into the church. The Palestinians refused to hand them over to Israel and Israel would not allow them to remain in Palestinian custody. Negotiators eventually agreed that the Americans would take the weapons, but even that was not easily resolved. "The Israelis wanted the weapons thrown in the Mediterranean, and the Palestinians wanted them thrown in the Dead Sea, closer to their territory,” then CIA director George Tenet wrote some years later.
“You can't make this stuff up," he quipped.

On May 10, a deal to end the siege was finally agreed upon and implemented. Thirteen Palestinians “with blood on their hands” walked out of the church and were flown in a British military plane to Cyprus, from where they went on to exile in European countries. Another 26 were sent to the Gaza Strip. The remaining Palestinians that had sought refuge in the church were questioned by Israeli security forces and subsequently released.

The siege was a diplomatic challenge for both Israel and the Palestinians. Israel was accused of not respecting religious sites and damaging the church during those five weeks in 2002. The Hamas and Fatah terrorists who holed up in the church were the subject to similar criticism.

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