As president, Rugova continued to support the nonviolent way to independence even when the armed resistance defenders formed the Kosovo Liberation Army to counter increasing Serbian oppression against ethnic Albanians. In 1998, Rugova won a second term as president, but was placed against the KLA when the war broke out in Kosovo. In 1999, he participated in the Rambouillet negotiations failed, as a member of the Kosovo delegation, seeking an end to hostilities. Having resided in the capital Pristina throughout his presidency, Rugova was taken prisoner by the state authorities after NATO began its air campaign against Yugoslav atrocities under US command in Kosovo. Rugova was exiled to Rome in May 1999 and returned to Kosovo in the summer of this year, shortly after the occupation of the KLA and NATO.
Rugova remained nominal president Bujar Bukoshi with his prime minister; Meanwhile, Hashim Thaçi, the former commander of the KLA, had led an interim government since April this year. However, the real power was in the hands of the United Nations administration. In 2000, Rugova and Thaci agreed to renounce their positions and work on the creation of PISG until the final status of Kosovo is decided. Rugova was elected president of Kosovo by the newly formed parliament in 2002 and 2005. Although his popularity before the war had declined, remained the country’s most powerful leader until his death from lung cancer in 2006 .
There were rumors that Rugova had converted to Catholicism just before his death. These rumors have never been confirmed by his family, or any other reliable source, and one of his closest collaborators, Sabri Hamiti, in an essay published on the first anniversary of his death, he refuted. Remember that Rugova, in terms of religion, called himself a “Muslim symbol”. On the other hand, the Chancellor of the Catholic Church in Kosovo, Don Shan Zefi, in an interview on national television in Kosovo, said he had dilemmas as to whether Rugova had converted to Catholicism and there Had no proof of his conversion and baptism. Zefi denied having baptized Rugova. Although he had a funeral service from the state, the head of the Islamic community of Kosovo, as well as many magnets they made an Islamic funeral prayer for the deceased. Its tomb, situated on the top of a hill in Prishtina, is oriented perpendicularly to Mecca, like all other Muslim tombs.