The episode starts with a short recap of the previous episode (which was the last episode of season 2): Tom Quinn shot Harry Pearce and then swam out into the North Sea, presumably to die.

The new material starts with a scene of Harry Pearce being rushed to the hospital.

Meanwhile, with MI5 agent Tom Quinn blamed for the death of the Chief of Defense, and with Tom's fellow MI5 agents tarred with his betrayal, the chairman of the Joint Intelligence Committee (JIC), Oliver Mace, sees this tragedy as the perfect opportunity to lay the ground-work for a merged single Ministry of Security with a political head and under the control of the government.

The MI5 team try to both prevent Mace from succeeding in his plan and try to prove that Tom Quinn is innocent. As MI6 agent Adam Carter notes, the best defense is to prove Quinn innocent. Carter has come over to help the injured Pearce run his section.

Will Tom be proved innocent? Will the “super-agency”get created over the ashes of MI5 & MI6 and the other intelligence agencies?