Thaci and three other ex-Kosovo Liberation Army commanders are charged with persecution, murder, torture and forced disappearances of people during and shortly after the 1998-99 uprising that eventually brought independence for the Albanian majority region from Serbia.
"The accused committed crimes against their perceived opponents to take control over Kosovo," prosecutor Kimberly West told the court in The Hague.
She added that in 1998 and 1999 more than 100 political opponents and perceived collaborators with Serbian security forces were killed and hundreds abused in and around 50 detention camps run by the KLA.
"This case is about the four accused's goal to gain and exercise control over all of Kosovo," West said near the end of a nearly three-year trial at the special Kosovo war crimes court in The Hague.
Thaci, 57, who served as prime minister, foreign minister and president of independent Kosovo between 2008 and 2020, and his co-accused deny all the charges.
Lawyers for Thaci, expected to give their closing statements on Wednesday, earlier argued that Thaci had no real authority over the KLA and its military commanders during the uprising and its aftermath and had to defer to local zone commanders.
West said on Monday prosecutors had overwhelming evidence showing that the four men on trial were key members of the KLA central staff and were the ones to issue orders to zone commanders, not the other way around.
Prosecutors say Thaci and other KLA leaders waged a violent campaign targeting political opponents, as well as minority ethnic Serbs and Roma to gain full control of Kosovo.
Most victims of persecution were members of Kosovo's 90 per cent ethnic Albanian majority, the prosecution said.
The Kosovo Specialist Chambers, staffed by international judges and lawyers, was set up in 2015 to handle war crimes cases under Kosovo law against ex-KLA guerrillas.
The war crimes tribunal was set up outside Kosovo because of worries about witness intimidation as former KLA leaders are seen as liberation heroes in the territory.
Despite these precautions, prosecutors said on Monday the trial had faced a "pervasive climate of witness intimidation".
Thaci and four other defendants face a separate trial for obstruction of justice which is scheduled to start on February 27.
More than 13,000 people, the majority of them Kosovo Albanians, are believed to have died during the late 1990s insurgency, when Kosovo was still a province of Serbia under then-nationalist strongman president Slobodan Milosevic.
The Kosovo court was created separately from the now defunct International Criminal Tribunal for the former Yugoslavia, also based in the Hague, which tried and convicted mainly Serbian officials for war crimes in the Croatia, Bosnia and Kosovo conflicts.
Milosevic also went on trial before the ICTY but died in 2006 before a verdict was reached.
