[2][3] Despite being the closest person to the President of Serbia Slobodan Milošević, with enormous impact on wartime events, he kept permanent contacts with all the factors involved in the conflict.
[2] Allegedly, he was removed in 1998 from the key intelligence position due to disagreements with Mirjana Marković and the Minister of Internal Affairs Vlajko Stojiljković, as he opposed the excessive use of force in Kosovo.
[1] Stanišić was prosecuted for war crimes in Croatia and Bosnia and Herzegovina in the period from 1991 to 1995, before the International Criminal Tribunal for the former Yugoslavia (ICTY) together with Franko Simatović.
[6] On 30 June 2021, he was found guilty under counts of murder, deportation, forcible transfer and persecution as crimes against humanity that occurred during the Bosanski Šamac ethnic cleansing, and sentenced to 12 years in prison.
He served as the deputy of head Zoran Janaćković within the newly established State Security Directorate of the Ministry of Internal Affairs of Serbia throughout 1991.
Allegedly, they were established for the purpose of undertaking special military actions in Croatia (Serb-controlled Republic of Serbian Krajina) and Bosnia and Herzegovina, intended to forcibly remove non-Serbs from those areas.
[10] After he was removed from the position in October 1998 due to disagreements with Mirjana Marković and Minister of Internal Affairs Vlajko Stojiljković, he was appointed as the National Security Advisor of Serbia.
[12] From 1998 to 2000, in a series of mafia wars during the last years of Milošević’s rule, most of the prominent members of the Serbian underground, some of whom took part in the paramilitary units, and security officers were murdered under mysterious circumstances.
After the assassination of Zoran Đinđić, Stanišić was arrested on 13 March 2003 during the Operation Sabre by the Serbian Police and handed over to the International Criminal Tribunal for the former Yugoslavia (ICTY) on 11 June 2003.
[15] However, his acquittal as well as that of Franko Simatović had been overturned on 15 December 2015 by a United Nations' ICTY Appeals Chamber which vacated the initial verdict deemed faulty as it was based on an insistence that the men could only be guilty if they "specifically directed" the crimes.
[5][18] After the MICT's retrial opening statements, Stanišić filed a request to follow the trial from home due to illness, which was granted and he has been on a provisional release since July 2017.
[22] He was found guilty of other crimes in Bosnia and Herzegovina (Bijeljina, Zvornik, Doboj, Sanski Most, Trnovo) and Croatia (Daljska Planina), and included in a joint criminal enterprise.
[23][24] The Tribunal concluded: ...the Trial Chamber found proven beyond reasonable doubt that, from at least August 1991 and at all times relevant to the crimes charged in the Indictment, a common criminal purpose existed to forcibly and permanently remove the majority of non-Serbs from large areas of Croatia and Bosnia and Herzegovina, through the commission of the crimes of persecution, murder, deportation, and inhumane acts (forcible transfer) charged in the Indictment...
The Appeals Chamber has further concluded that all reasonable doubt has been eliminated that Stanišić and Simatović possessed the requisite mens rea for joint criminal enterprise liability.
[25]The United States Central Intelligence Agency (CIA) submitted a sealed document to the court attesting to his role as an undercover operative helping to bring peace to the region.