Farroukh was working with MI-5 when the bombing occurred. His son Emir is the only one who can prove that in court. Martin and Claudia successfully get Emir to the courthouse, but the case is closed before he can testify because his father was killed in prison.
The Borough Market in London is blown up in a terrorist act, and Farroukh Ergodan is arrested and charged with being the mastermind of the act. Six months later, his trial is set to begin. Due to the sensitive nature of the evidence, the defense is split into two groups. One will defend Farroukh in open court, while another is to deal with classified information in a closed court. The information in the closed court will be determined by the judge whether or not it can be used in open court. Martin Rose (Eric Bana) is the barrister chosen by the Attorney General (Jim Broadbent) to handle the open court part (replacing another barrister who died), and Claudia Simmons-Howe (Rebecca Hall) will handle the closed court part. The two are not to have any communication with each other, so as to not compromise the case. The two once had an affair, and if that became known, the case would be declared a mistrial and their careers would be ruined. They have since broken up.
Martin and Claudia separately investigate the case, and both notice that they are being followed. Martin learns that Farroukh was planted into the terror cell by MI-5 in order to prevent an attack, but it occurred anyway. Since MI-5 inadvertently funded the attack, they are doing whatever it takes to prevent that knowledge from going public, including killing the previous barrister. He secretly passes this information to Claudia, and she brings it up in the evidentiary hearing. While questioning an MI-5 agent, she learns that Emir, Farroukh's son, is an informant. The judge then demands that Emir be brought in the next day for questioning.
MI-5 now knows that Martin and Claudia know the truth, and will try to stop Emir from being questioned. They go from following Martin and Claudia to attempting to kill them. Martin survives a deliberate car crash, and Claudia is attacked in her home, but escapes. Meanwhile, Emir, the only person who can prove his father was working for MI-5 and is not a terrorist, realizes that he now a target and attempts to flee the city. Martin and Claudia, now working together, track him down and are able to get him to the courthouse the next day. But before he can be questioned, the judge closes the case. Farroukh hung himself in prison (actually killed by MI-5 and made to look like a suicide), so there is no need for anymore testimony. Afterward, the Attorney General tells Martin that if either he or Claudia attempt to tell their story to anyone, he will reveal not only their affair, but that they worked together even though they weren't allowed to. The resulting scandal would ruin their lives.
The movie ends three months later. Martin and Claudia have restarted their relationship, and MI-5's cover-up was somehow revealed. The Attorney General is in Parliament, and he is getting ripped to shreds by the House members about orchestrating the cover-up.