Two Indian agents, working under Ranvir Singh (Manoj Bajpai), are chasing an international arms dealer Mikhail, but instead he kills them both and escapes. A year later Shabana Khan (Taapsee Pannu) a college student who is also a Judo fighter is being followed by Indian agencies as a potential recruit. Shabana had a past of being kept in a  juvenile home for killing her abusive father who used to physically assault her mother.


One fateful night, Shabana goes out on a dinner date with her friend Jai on his birthday. During their bike ride home, Shabana faces eve teasing from a group of four drunk men in a jeep. Later it turns into a physical altercation resulting in Jai getting killed and men running away. Soon after, Shabana receives a call from an unknown number asking if she wants to avenge her lover's death. The unknown caller agrees to help her persecute the killers in exchange for Shabana joining a secret agency. Shabana agrees to this and accordingly receives information on the killer's whereabouts and aids her in killing them. Shabana then reaches Goa to the same hotel were the main culprit who killed Jai was staying. As instructed Shabana enters his room, killing him and later escapes with the help of Ajay Singh (Akshay Kumar). The unknown caller is revealed to be Ranvir Singh.


Following this Shabana is recruited into the secret agency on a trial basis, wherein she is to receive extensive training in physical fitness and fighting techniques. The story then focuses on a global arms dealer and supplier called Mikhail, who has been on the radar of several intelligence agencies. Three Indian Agents then track down Tony considered as Mikhail's right hand. During interrogation Tony tips them a German Doctor's name who has surgically changed Mikhail's face. By the time agency contacts the Doctor to get Mikhail's new look, Tony kills all three agents and escapes, revealing that he himself is Mikhail (Prithviraj Sukumaran).


Ranvir Singh gets the tip that Mikhail is planning another plastic surgery to change his face again. This time Shabana is sent to kill Mikhail, with the help of Ajay Singh and Om Prakash Shukla (Anupam Kher). Shabana enters the hospital disguised as a patient. After getting rid of Mikhail's private security, Shabana is about to kill Mikhail in OT. To her surprise Mikhail is very much awake as he had refused to take anesthesia during the operation. After quite a tussle, Mikhail almost strangles Shabana. But finally Shabana manages to kill Mikhail and escapes from the police, once again with the help of Ajay. Together, they successfully complete the mission and also she avenges Jai’s death as well.

Naam Shabana
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