On September 1, 2013, he was reappointed as acting Director[2][3] due to the health problems suffered by Asadullah Khalid following an attempted assassination.

After two years, he was appointed as Deputy National Security Advisor and then he rejoined the NDS as acting General Director in September 2013.

The president said he wanted to keep the service term short, but Mr. Nabil publicly announced that President Karzai asked him to resign due to their disagreements over policies, such as torturing, misbehaving, and discrimination against detainees during the persecution process The President was also not happy because he thought Mr. Nabil was failing to stop Taliban influence in Afghan security forces as they were hiring spies that caused fatal casualties and harm to security forces.

The insurgents were improving their tactics and finding new ways to damage and inflict higher casualties on the Afghan security forces and destroy the infrastructures and government facilities.

They were making homemade bombs, and improvised explosive devices, buying weapons from Afghan security forces, weapon and drug trafficking, suicide attacks, and drug trafficking which provided financial support that inflicted heavy casualties on the forces.

This brought  Nabil's capabilities of handling the intelligence agency under serious questions, so President Ghani stepped him down.

He has received an appreciation letter from the Afghan Civil Society Association, for his effective efforts in the implementation and oversight of human rights in all NDS detention center.