The Musharraf government claimed Taliban leader Baitullah Mehsud masterminded Bhutto's assassination. The U.S. government agreed, the CIA's chief at the time, Michael Hayden, told media outlets in 2008 including The Washington Post. Mehsud was killed by a Predator drone attack in September 2009.

In 2010, the United Nations concluded Bhutto was probably killed by al-Qaida and its Pakistani Taliban allies who recruited the 15-year-old suicide bomber. It also said that the government of military leader Musharraf ignored Bhutto's requests for better security and then tried to cover up the alleged crime. In 2013, Musharraf was arrested on treason charges including alleged involvement in Bhutto's murder. As of May 2014, the cases were still pending.

"We will probably never know with full certainty who killed Bhutto. The list of people and groups that considered Bhutto a hated enemy is long. There are pieces of the murder puzzle but painfully few elements to put them all together," Munoz wrote. "It may well be that Bhutto's assassination will be another unsolved case in the long history of impunity in Pakistan, and that the controversy surrounding her assassination will endure as much as her memory."