He was the operational chief of Hizbul Mujahideen, an Islamist, Pro-Pakistan militant organization active in India's Jammu and Kashmir.

[7] During the 2010 unrest, he was detained by the Indian security forces for alleged support to separatist pro-freedom militants and protesters.

[8] In 2017 he became the commander (de facto chief) of Hizb-ul-Mujahideen in Jammu and Kashmir after the death of Burhan Wani and the defection of Zakir Musa.

[9][10][11] In March 2014, he was alleged to be involved in the killing of a Sarpanch's father, Haji Ghulam Mohd Dar in Dogripora.

[3] Naikoo started the practice of offering gun salutes to militants killed in encounters and posting them on social media.

Naikoo's last audio message in April was related to the COVID-19 pandemic where he requested people to follow medical advice to keep themselves protected.