[3] Starting 2007, Ali's charges in the Kenyan police began severely cracking down on the notorious Mungiki sect, a local politico-religious group and banned criminal organisation known for, among other things, decapitating policemen.

[4] For this perceived excessive use of force on its part, the police drew heavy criticism from human rights groups, particularly over the deaths of several hundred youth in its custody without trial over alleged links to the sect.

[5][6] In 2008, controversy also surrounded the Kenyan Police's response to the violence that rocked the country following a disputed presidential election, especially regarding a "shoot to kill" order that was alleged to have come out of Ali's office.

The ICC prosecution alleged that Ali authorised the use of excessive force and facilitated attacks against supporters of the opposition Orange Democratic Movement during the period's post-election violence.

[10] Alston reported that there was abundant evidence linking Ali to a central role in devising and overseeing the policy of extra-judicially executing large numbers of suspected criminals.