The scene begins with a state funeral service, held in memory of the late Senior Superintendents Albert Kwong and Vincent Tsui, both killed in action during Operation Cold War. After the funeral service, Police Commissioner Sean Lau (Aaron Kwok) receives a call from one of the culprits of the missing Emergency Unit (EU) van, who has kidnapped Lau's wife. He instructs Lau to release Joe Lee (Eddie Peng) from prison in exchange for the return of his wife.
To rescue his wife, Lau decides to override police Standard Operating Procedure and protocol and enacts an Emergency Response protocol, transferring Joe out of prison. After informally transferring management power to his subordinates and taking personal responsibility for the entire operation, Lau follows the instructions from the kidnapper to transport Joe to an MTR station. However, Joe manages to escape from the scene with aid from several accomplices, who also set off a bomb in the station. Lau finds his wife injured but otherwise safe. Following the bombing incident, media and politicians immediately start demanding a Public Inquiry on the operation. Out of fear that the force has been infiltrated, Lau privately requests Billy Cheung (Aarif Rahman), the ICAC investigator who helped him previously, to form a "Clean Task Force" independent of the police force to track down the perpetrator.
Meanwhile, M.B. Lee (Tony Leung Ka-fai), deputy police commissioner who is on pre-retirement leave, is introduced by his son Joe to Peter Choi (Chang Kuo-chu), former police commissioner who is now a businessman providing IT equipment for the police force. Choi reveals that he was the real mastermind behind the disappearance the of EU van, and is Joe's backer. Choi convinces Lee to join him in a plan to remove Lau as commissioner and replace him with Lee; Lee reluctantly agrees after being urged by Joe.
The Public Inquiry at the Legislative Council is underway to determine the lapses on Operation Cold War and current actions of Lau. Independent Legislator Oswald Kan SC (Chow Yun-fat) is convinced by his old friend Lai (Waise Lee), the Secretary of Justice, to participate in the committee, but vows to act independently. At the first hearing, Kan realizes that Lee is trying to emphasize Lau's failure during the operation, and deduces that there must be an ulterior motive behind his change in stance. He sends out his protégée, Bella Au (Janice Man), to investigate.
Au secretly tracks Lee to a meeting with Choi, Joe and their associates, and photographs their meeting. She then follows Choi as they leave the scene. Noticing that they were followed, Joe opens fire at Au's car, causing a chain collision in a tunnel. Sean Lau, who is also tracing them, arrives at the scene and engages in shootout with the terrorists. Choi's vehicle escapes, but Joe Lee is shot down and apprehended by Lau. Au is killed in the shootout, but her photographs reveal Choi's association with M.B. Lee and Joe Lee. As the victims are taken to the hospital, a confrontation occurs between Lau and Lee, who is angry that Lau has seemingly killed his son. Kan steps in and warns both of them of their errors, while blaming Lee for the death of his protégée. Spurred by vengeance, Lee launches his campaign to unseat Lau. Meanwhile, Kan and Lau share work force and intelligence in order to tackle down Lee.
Lau manages to gather five gazetted police officers in petition for removal of Lau from the office of police commissioner. In the final hours before Lau officially steps down, he reveals information gathered by Cheung and Kan, and launches a counter plan to locate the missing EU van and apprehend the criminals at large. Secretly knowing that Lee is collaborating with them, Lau forces Lee to supervise the operation. The operation is a success, with all of the suspects killed while believing that Lee has betrayed them. Lau confronts Choi at the Hong Kong International Airport as he tries to escape. He tells Choi to leave, never to return to Hong Kong ever again, in exchange for the Police not pressing charges against him.
Lau delivers a public speech on the independence of the Hong Kong Police Force, having survived the Public Inquiry. Meanwhile M.B. Lee, forced to retire permanently, looks after his son, who is revealed to be still alive and in critical condition in hospital.