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Marwan Kawasme and Amar Abu Aysha/COURTESY

After a three-month manhunt, Israel tracked down and killed the two main suspects in the June kidnapping and murder of three Israeli teenagers, in a shootout at their hideout in northwest Hebron early on Tuesday.Before dawn, soldiers backed by the Border Police Counterterrorism Unit (Yamam) and the Shin Bet (Israel Security Agency) surrounded the building in Hebron where Marwan Kawasme and Amer Abu Aysha had been hiding in recent days.Both suspects were longstanding Hamas members who had been holed up in a carpentry shop in Hebron.Security forces surrounded the structure after learning that the two were hiding in a pit located in the basement.Soldiers fired at the walls of the structure and called on the suspects to surrender, but those calls were ignored.“We wanted to arrive from the advantage of height, because we did not want to encounter them on the same floor and conduct face-toface combat,” said Brig.-Gen.Tamir Yadai, commander of the IDF’s Judea and Samaria Division.“At a certain stage, they came out and opened fire,” Yadai said. “One was killed on the spot, and one fell into a pit and I assume he was killed,” Yadai added. Members of the Counterterrorism Unit hurled grenades into the pit. Both bodies were later recovered and positively identified.Yeshiva students Gil-Ad Shaer, 16, Eyal Yifrah, 19, and Naftali Fraenkel, 16, were kidnapped by the two terrorists late at night on June 12 from a hitchhiking post in Gush Etzion. Their bodies were found nearby more than two weeks later on June 30. In June, both Kawasme and Abu Aysha were identified as suspects by the Shin Bet, which added that both were wanted as soon as the security forces learned of the kidnapping.The families of the three teenagers released a statement in which they said they were glad the security forces and the government had been steadfast in their resolve to bring the killers to justice.“An evil circle has closed and we are beginning a new year in which we hope only good circles will open,” they said. “We want to wish the nation of Israel a good and sweet year. And we want to thank all those at home and abroad who have embraced and supported us.”Yadai said security forces “have been pursuing Marwan and Amar since June 20. This has been a long and complex operation involving the Shin Bet, the IDF, and the Counterterrorism Unit. Yesterday evening we located their hiding spot, and since 1 a.m. we surrounded it.”Security forces received intelligence information about the hideout over the past week, he added. One of the suspects was armed with an M-16 and the second came out shooting with a Kalashnikov.“They did not hide in this location for the entire time,” he said.“We believe they were there over the past week.The carpentry shop is located south of Al-Danadi Hospital in Hebron, and is near a Kawasme family-owned complex.IDF Chief of Staff Lt.-Gen.Benny Gantz spoke with OC Central Command Maj.-Gen.Nitzan Alon and congratulated him on the successful operation on Tuesday.“On the eve of the New Year, Operation Brother’s Keeper, which began on June 13 and lasted throughout this time with determination, has ended,” Gantz said. The IDF had promised the families of the victims that they would reach the kidnappers, and kept the promise, Gantz said.“There is no comfort for the families in their heavy mourning and pain, but I hope they have a little relief in the knowledge that we got to the murderers of their sons,” Gantz added.Early in the morning, security forces notified the parents of the three Israeli teenagers that the two men who were believed responsible for the death of their sons had been killed.“Their day of judgment has come,” Eyal Yifrah’s father Uri told Channel 2 News. His mother, Iris, added: “we prayed and waited for this day to come.”Rachelle Fraenkel, mother of Naftali, told the media she was relieved she had been spared the sight of the two men smiling in court or released in a future prisoner deal.“We were afraid they would hurt more innocent people,” she said. “We are pleased that this resolved without any injuries to our soldiers.”An officer from the special forces personally visited the Fraenkel home on Tuesday to update them about the end of the manhunt.These last months there was always a sense that matters had been left hanging, he said. “I am thankful to God, that our mission was completed and that I had the privilege to be there and to command a combat unit that could produce these results,” he said.“We weren’t looking for glory, nor do we want it,” the officer said. “We just wanted to do our job properly. It’s hard to explain, but I had always believed and hoped we would arrive at this moment.”Hamas spokesman Sami Abu Zuhri said in Gaza that the organization “praises the role martyrs Abu Aysha and Kawasme played in chasing down Israeli settlers and we stress that their assassination will not weaken the resistance.”The governor of Hebron, Kamel Hmeid, confirmed on Palestinian radio that the two were dead.“It’s clear now the two martyrs, Kawasme and Abu Aysha, were assassinated this morning during a military operation in the Hebron University area,” he said.“We condemn this crime, this assassination, as deliberate and premeditated murder.”A poster published by Hamas on Tuesday described the two as “heroic Kassam martyrs” and “heroes of the operation of capturing and killing three occupation soldiers.”Kawasme, 29, a Hamas member and son of a family of Hamas members, had been arrested multiple times in the past for terrorist activities, including most recently in 2010, after being identified as a member of a Hamas terrorist cell that carried out an attack in which four Israelis were murdered.Abu Aysha, 32, a Hebron-based Hamas member and son of a family of Hamas members, was in Israeli custody from 2005- 2006 on suspicion of being involved in terrorism.In August, the home of Abu Aysha was demolished by combat engineers supported by Border Police officers. Security forces also sealed off a home belonging to Kawasme.After the two suspects were killed, clashes broke out in Hebron between Israeli security forces and young Palestinian men and teens, some of them masked.Dozens of Palestinians, some using slingshots, hurled stones at the soldiers who replied with smoke grenades. At least one wounded Palestinian was seen carried away by his fellow protesters to an ambulance which arrived at the site.At the scene of the earlier shootout, smoke billowed from the charred building where smoldering fire kept on burning near a huge hole in the floor. One Palestinian man picked up a smoke grenade which hit the ground and threw it towards the troops who fired riot dispersal rounds from a nearby corner.A mass funeral for the two men was held in Hebron, in which their bodies were paraded through the streets to the cemetery on gurneys. Amar Abu Aysha’s mother helped carry his body to its final resting place.Outside Hebron, Palestinians cut an electricity line to the settlements in the South Hebron Hills.Also on Tuesday, security forces arrested Basher Kawasme and Ta’ar Kawasme, the sons of Arafat Kawasme, himself under arrest since July 14 on suspicion of helping the murderers hide after killing the three Israeli teens.“In recent days, a number of Hamas operatives suspected of abetting the suspects have been arrested and taken to the Shin Bet for questioning,” the intelligence agency said. Two months ago, the Shin Bet arrested Hussam Hassam Kawasme, a Hamas operative who confessed to acting as the cell commander and securing the funding for the kidnapping and murders from Hamas members in the Gaza Strip.Hussam Hassan Kawasme, the alleged mastermind, was indicted in the Ofer Military Court on September 4. The Shin Bet arrested him on July 11, on suspicion of assisting the killers and of hiding the victims’ bodies in land he owned in Hebron, security forces said. He is described in the indictment and by the Shin Bet as a command-level Hamas operative, who obtained funding for the kidnapping from his brother, a Hamas member whom Israel expelled to the Gaza Strip as part of the Gilad Schalit deal.Tovah Lazaroff and Reuters contributed to this report.