Wanchoo was assassinated by "unidentified gunmen" on 5 December 1992.[4] Local activists accused the government of having released two militants in exchange for an extrajudicial execution, one of whom would be killed in an "encounter"; Human Rights Watch noted Wanchoo's murder to fit into the state's brutal suppression of conversations on human rights.[4] Days before his death, Wanchoo had confessed in private, about threats to his life from local administration as well as the security apparatus.[5]
Within days, the state government roped in Central Bureau of Investigation (CBI) to investigate the murder[6] who concluded a local militant group called "Jamait-ul-Mujahidin" — comprising twelve Kashmiri Muslims — to have planned the assassination.[7] However, by the time the investigation concluded, four of the accused had died and five had absconded, leaving only three — Ashiq Hussain Faktoo, a budding separatist; Mohammad Shafi Khan, a faculty member of the University of Kashmir specialising in Persian; Ghulam Qadir Bhat, a constable with the Jammu and Kashmir Police[8] — for trial under Terrorist and Disruptive Activities (Prevention) Act before a special court in Jammu.[9][7] Confessions were obtained from all of them.[7]
In July 2001, the TADA Court acquitted Faktoo and others in light of procedural deficiencies in obtaining confessional statements and the absence of any other corroborative evidence.[9][7] CBI appealed the judgement before the Supreme Court of India[a] and in January 2003, S. N. Variava disagreed with the court's characterization of the confession, sentencing all to life-imprisonment.[9][7] Faktoo and Khan filed a review petition but the Court rejected re-adjudication, in September of the same year, after a closed-court hearing.[10]
The judgement appears to be unconvincing among scholars; Seema Kaji and Sumantra Bose continue to suspect the Indian state to have had a role in the murder.[11][12]