Aiyaary is the story about the armed forces of India and the corruption that has set in in the ranks of the forces. Army chief Pratap Malik (Vikram Gokhale) has clandestinely set up a covert army unit under Colonel Abhay Singh (Manoj Bajpayee), allocating funds to it although he has no authorisation to do the same. Major Jai Bakshi (Sidharth Malhotra) is a part of the covert team and he is a promising young army officer who is very inspired by the principled Colonel and his philosophies of life. It emerges that Colonel Abhay Singh and Major Jai Bakshi have disappeared. Army officer K. Srinivas (Rajesh Tailang) is interrogating Maya (Pooja Chopra), another member of the covert team of Colonel Abhay Singh, about the whereabouts of the two.
As the drama unfolds, it turns out that Jai has stolen sensitive data from the covert unit’s data centre and he also has the recorded conversation between the army chief and Lieutenant General (retd.) Gurinder Singh (Kumud Mishra). Jai has learnt the art of decoding data from hacker Sonia (Rakul Preet Singh) whom he has ultimately fallen in love with. In the taped conversation, Gurinder can be heard offering army chief Pratap Malik bribe money to clear the arms and ammunition deal offer received from an arms supplier in Czech Republic. But the upright Malik won’t do it as the cost of the deal is four times what it should be. Gurinder Singh, before concluding the conversation, has threatened to expose the covert unit and the army chief if he (army chief) does not close the arms deal. Armed with so much incriminating evidence, Jai has fled the country.
Does Mukesh Kapoor eliminate Jai? Or does Abhay Singh kill Jai? Is Mukesh Kapoor exposed? Does Gurinder Singh expose the army chief or does Abhay Singh prove one-up on him and expose him before that? Is Jai Bakshi working against the interest of India? Why does Jai Bakshi ask his boss, Abhay Singh, to meet Baburao (Naseeruddin Shah) who is holed up in a small hotel in India? Who is Baburao and what explosive information does he have? Whom will this information expose? Is what forms the rest of the film.