A Pakistan military group under Maj. Abdul Jalal Rana trespasses Indian waters targeting New Delhi. The plan is intercepted by Dr. Emma John of Intelligence Wing who informs it to her senior Padmabhushan Dr Sudarshan (Nedumudi Venu). Though Dr. Sudarshan tries to contact Home Minister, his Secretary (Sreekumar)snubs him by saying that its crazy to wake the minister up late at night and agrees for a meeting on the next morning. Dr Sudarshan offers Dr Emma a ride back home as it is too late for her to catch the metro train. Kishore Balakrishnan (Vijay Menon), the senior analyst at the agency, is seen pushing the mobile jammer button and calling Swamini Bodheswari who was calling an Income Tax Commissioner to not order arrest on a person. On the way back home, Dr Sudarshan and Emma is chased and pulled over by two cops who shoots them down. Unbeknownst to them, Imran, a photo journalist manages to click the pictures in his camera. The cops take with them some documents before leaving the crime scene where they are joined by Shankar Ramdas (Devan), a senior police officer. Kishore sets off to see Swami Chandramoulishwar (Saikumar)at his ashram demanding Rs 2 cr for the information he passed before. But Swami suffocates him till he passes out before pushing him to Yamuna.

The bodies of Dr Sudarshan and Emma are found next day on the banks of river Yamuna in an intimate position. A few metres away another dead body of Kishore is found drifting. Police concludes that Kishore who was madly in love with Dr Emma John killed both Dr Sudarshan and herself out of jealousy and then killed himself by drowning in the river. Raman Madhavan (Jayan), the director of NID pays a visit to Swami Chandramowlishar's ashram where he is met with some foreign arm traders. They conclude that if the PM is alive the deal wont take off and it has become highly necessary for the PM to give way for Raman Madhavan. Swami takes Raman Madhavan to meet Rana and his men disguised as Swamis.

G.K (Janardhanan), the central home minister assigns Joseph Alex I.A.S (Mammootty) to investigate the death of Dr Sudarshan. He shrugs of the findings of Forensic Director and analyst and asks them to give a fresh report with the facts they have excluded deliberately before. He comes out of the Forensic building and is shocked to find a mysterious man in black leather jackets walking away from his car and getting into another. Joseph gets a call from Nanda (Samvrutha Sunil), the daughter of Home Minister, who is also a news journalist, who shows him the picture of a cop holding a gun towards someone inside a white car. Imra, who had clicked this photo has a gut feeling that he has seen Dr. Sudarshan in that car.

Bharath Chandran IPS (Suresh Gopi) is assigned to assist Joseph in investigation. Both Joesph and Bharath get Shankar arrested. But in court, Shankar is killed by henchmen of Swami. Meanwhile Joseph is called into the PMO to be told that he is off the case now. He retorts to the personal Assistant to PM when the latter tries to taunt him but is stopped by Home Minister. Joseph requests Privacy with PM to start off another lengthy argument that culminates in allowing him to continue with the case. Also he makes the PM understand that if something were to happen to him, the nation will suffer huge financial loss for the burial and following elections and other things and it is these expenses Jospeh is concerned about rather than PM's Life. Swamiji gets pissed off at the PA on this. He decides its vital to assassinate the PM to make Raman Madhavan the next PM by ensuring support from many coalition party leaders. He gives Rana the green signal to kill PM and fixes the date. ACP Arjun captures the PA coming out of Swami's Ashram by disguising as the driver. The next day the PA is taken into custody where he is interrogated by K&C. Soon after they leave, the pak army men pretending as Delhi Police comes in and asks for PA's custody, but then they draws the gun out and shoots ACP Arjun on the head. In the ensuing fight Ubaid manages to kill several Pak officers but Rana himself shows up and kills both Ubaid and the PA. Enraged Bharath storms into the Ashram where he is held at gunpoint by Swamis men after few minutes of verbal exchange. Joseph appears right in time to save Bharath from getting killed and tells Swami that he is not an idiot to come alone. After a few dialogues, Swami is taken into custody and informs him that they are not going to put him into a trial. Later Raman Madhavan too is taken into custody at the middle of night by the officers. They track down the location of the ISI agents in the middle of a deserted place. Both Swami and Raman Madhavan are taken to that place and the people accompanied them are shot dead in front of the building. Minutes later Bharath and Joseph arrives with a team of commandos and the sneaks into the dilapidated cottage where they bumps of several baddies. At last the confront Rana who initially overpowers them. But after getting thrown away by Rana, both draws strength to kick the hell out of Rana. After a brief stint of dialogue delivery Joseph draws the gun at him and shoot Rana 3 times. Then Bharath draws the gun and after telling a few words he too shoots Rana another 3 times in the leg. Then Joseph comes close to Rana and quips at him before sticking a flag pole into his chest chanting 'Bharath Mata ki Jai'. They both turns to Swami and Raman Madhavan and locks them up in the car and fixes a bomb on it. The bomb explodes after they getting out of the building, killing both Swami and Raman Madhavan.

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