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The president of Kosovo, Hashim Thaci, a guerrilla leader during Kosovo鈥檚 war for independence from Serbia in the late 1990s, resigned on Thursday and will face charges for war crimes and crimes against humanity at a special court based in The Hague.

Mr. Thaci said he was taking the step 鈥渢o protect the integrity of the presidency of Kosovo鈥� and to preserve the historical truth of who was perpetrator, and who victim, in the conflict.

鈥淲e are a freedom-loving people and not vengeful,鈥� Mr. Thaci said at a news conference in Pristina, Kosovo鈥檚 capital. 鈥淭hat is why no claim may rewrite history. Kosovo has been the victim. Serbia has been the aggressor.鈥�

Mr. Thaci was indicted in June along with nine other former rebel leaders by a special Kosovo court and associated prosecutor鈥檚 office based in The Hague, Netherlands, which were set up five years ago to investigate and try former ethnic Albanian rebel leaders for alleged war crimes. The charges include murder, enforced disappearances, persecution, and torture.

The 1998-1999 war killed more than 10,000 people 鈥� most of them ethnic Albanians 鈥� and 1,641 people are still unaccounted for. It was brought to an end by a 78-day NATO air campaign against Serbian troops.

Among others charged with committing crimes during and after the war is Kadri Veseli, a former parliament speaker and an opposition party leader, who said he planned to travel to the The Hague on Thursday and was resigning from 鈥渁ll public political activities.鈥�

Both Mr. Thaci and Mr. Veseli have denied committing any crimes.

Mr. Thaci, a commander of the Kosovo Liberation Army during the war, said he was proud to have belonged to that force, calling it 鈥渢he most sublime value of the Albanian nation.鈥�

He called the indictment 鈥渢he smallest price we have to pay for the freedom of our people.鈥�

The government said in a statement that all defendants should be considered innocent unless the court decides otherwise.

鈥淣o one may judge our fight for freedom,鈥� the government said, adding that the KLA 鈥渇ought for the liberation of our country, to protect the house and not in a foreign land, and as such it has the support of the international community.鈥�

Mr. Thaci held a ceremony at his office to hand over his presidential duties to parliament speaker Vjosa Osmani. The government said the 鈥渃onstitution and the laws in power guarantee a clear transition of powers and exercising the responsibilities without any institutional vacuum.鈥�

Mr. Thaci was elected president in February 2016. His current term ends in April, when the national Assembly of Kosovo was expected to elect a new president.

Amnesty International鈥檚 Balkans researcher, Jelena Sesar said the indictment of Mr. Thaci and the nine others would give hope to 鈥渢housands of victims of the Kosovo war who have waited for more than two decades to find out the truth about the horrific crimes committed against them and their loved ones.鈥�

The European Union issued a statement welcoming Mr. Thaci鈥檚 cooperation with the Hague-based legal institutions, saying it 鈥渟trongly supports the work of the Kosovo Specialist Chambers and the Specialist Prosecutor鈥檚 Office.鈥�

鈥淔ull cooperation with these institutions is essential as an important demonstration of Kosovo鈥檚 commitment to the rule of law, which in turn is a core element for Kosovo鈥檚 progress on its European path and for EU鈥檚 engagement with the Western Balkans as a whole,鈥� the EU statement said.

The prime minister of Albania, which borders Kosovo, expressed his country鈥檚 support to Mr. Thaci in 鈥渢his battle for Kosovo and the inviolable justice of the liberating war.鈥� Prime Minister Edi Rama described the indictments as resulting from an 鈥渁bsurd process that will finally stamp the KLA clarity and the inability to rewrite its history.鈥�

Exact details of the 10-count indictment against Mr. Thaci, Mr. Veseli, and the others have not been released. Announcing the existence of the indictment earlier this year, the Specialist Prosecutor鈥檚 Office alleged that the men were 鈥渃riminally responsible for nearly 100 murders.鈥�

At the time, the prosecutor鈥檚 office said it made the existence of the indictment public because of what it called repeated efforts by Mr. Thaci and Mr. Veseli 鈥渢o obstruct and undermine鈥� the work of the court and said they were believed to have tried to overturn the Kosovo law that created the court.

The formation of the court and prosecutor鈥檚 office followed a 2011 report by the Council of Europe, a human rights body, that included allegations that KLA fighters trafficked human organs taken from prisoners and killed Serbs and fellow ethnic Albanians.

Ms. Sesar, the Amnesty International expert, said that a 鈥渃ulture of impunity鈥� had persisted in Kosovo since it has taken nearly 10 years for those suspected of criminal responsibility to be brought to court.

After the war, Mr. Thaci created the Democratic Party of Kosovo and has been foreign minister, deputy prime minister, and prime minister, and now president since April 2016.

Kosovo-Serbia ties are still tense 21 years after war鈥檚 end, despite nine years of negotiations mediated by the European Union and supported by the United States.

The indictment was announced in June when Mr. Thaci was en route to a meeting at the White House with Serb counterpart Aleksandar Vucic. That meeting was held with Kosovo鈥檚 prime minister instead in September.

In 2008, Kosovo declared its independence from Serbia, a move that Serbia refuses to recognize.

This story was reported by The Associated Press. Semini reported from Tirana, Albania. Mike Corder in The Hague, Netherlands, and Lorne Cook in Brussels also contributed reporting.