In 1960s, after India has endured two conflicts within a space of five years, renowned Indian nuclear physicist, Dr. Homi J. Bhabha, makes a public statement advocating India to become a nuclear power. This draws the attention of the CIA, which begins covert operations to sabotage India's nuclear program.
A junior operative in Indian Intelligence Bureau, Vishnu Shankar uncovers the classified details about Bhabha's travel plans having been leaked to American agents, he races to thwart an impending assassination plot. Despite his efforts, Bhabha dies when his flight to Geneva explodes in 1966, effectively stalling India's nuclear program. This event leads to creation of Research & Analysis Wing, India's specialised espionage organisation in enemy territories, headed by R. N. Kao.
In 1972, in the aftermath of the Shimla Agreement, Pakistan's Prime Minister Zulfikar Ali Bhutto decides to scale up his country's nuclear program. Kao gets this intelligence from his counterpart in Mossad, and sends his intelligence agent, Vishnu Shankar to Islamabad on a covert mission to sabotage Pakistan's nuclear program. Once in Islamabad, Vishnu gets to work in finding out where Pakistan is building its nuclear facilities.
Meanwhile, Murtaza Malik, head of ISI, has taken on the task of cleaning out foreign secret operatives in Pakistan. He is brother-in-law and colleague of brigadier Naushad Ahmed, a high ranking official in the Pakistani Army. Naushad is an informant to R&AW under duress, and supplies the crucial information to Vishnu Shankar that Pakistan is buying nuclear reactors instead of creating them from scratch as previously assumed. Soon after, Naushad is caught and killed by Murtaza.
Naushad's intel changes the focus of Vishnu's mission to tracking down who Pakistan is buying the reactors from. Through his covert operatives, Sukhbir (operating under the false identity of Karachi Stock Trader, Rafiq) and Vikram operating in Paris, he figures out that Pakistan is making secret payments to a French company, HGN, to secure these reactors. Vikram, collaborates with his Mossad counterpart, Maria, and two other R&AW agents in Paris to track and murder the ISI agent in charge overseeing these payments.
In Islamabad, Vishnu seeks to fill the void left by Naushad's death. He recruits Fatima Khan, the Editor of Haqeeqat newspaper who is critical of the ongoing regime and is the niece of Munir Khan, the nuclear physicist leading Pakistan's nuclear mission. With Fatima's intel, Vishnu obtains the time and location of the incoming shipment from France that contains disassembled nuclear reactor, and blows up the ship, losing four Indian agents and several Pakistani soldiers in the process.
The end credits chronicle that India tested its first nuclear weapon shortly afterwards, in 1974, and Pakistan in 1998 - 24 years later.
