Hussain's throat was slit; he had also been stabbed 28 times and strangled, according to police statements reported in the local press. His body was found with both hands and feet tightly bound.
On March 11, two days before Hussain's body was found, the wife of another cartoonist reportedly received a threatening phone call from someone who claimed to be a member of the Shiv Sena, a Hindu nationalist political organization. The caller allegedly claimed that the Shiv Sena was responsible for Hussain's murder, and that her husband, Paresh Nath, a cartoonist for the newspaper National Herald, and Sudhir Tailang, a cartoonist for the newspaper Hindustan Times, would be targeted next in reprisal for their cartoons mocking leaders of the Shiv Sena and the ruling Hindu nationalist Bharatiya Janata Party.
Peter Popham wrote in London's The Independent that one of Hussain's "typical recent [cartoons], published when Hindu-Christian antagonism was running high, showed a demonic little [Hindu nationalist] figure squatting on a cross being dragged by a ragged, Christ-like figure inscribed SECULARISM: foretelling the end of secular values in an era under the sway of Hindu extremists."
On November 27, police told reporters they had arrested a seven-member gang of car thieves who had confessed to the murder.