Season 3 finds Scott and the mysterious agent Rachel Dalton in the Kenyan desert securing the transfer of a Libyan functionary seeking asylum. Back in Britain, Stonebridge is training Section 20 recruits. Nothing goes as planned for either of them.
Taken hostage in Mogadishu by Waabri and his girlfriend Asmara, Scott and Dalton escape with the help of Stonebridge and Richmond. Sinclair is replaced as leader of Section 20. Michael and Kerry rekindle their relationship.
El Soldat's forces are preparing to assault the farmhouse where Stonebridge, Scott, Markunda, and Othmani are holed up. Sinclair continues to question Dalton's command style. Karl Matlock continues to make inroads to acquire the triggers.
Section 20 races to intercept a former South African nuclear scientist, Peter Evans, from Matlock. At the airport, they run into a team of Mossad agents who want to kill Evans. Section 20 learns that Knox is behind loss of the triggers.
Lilian Lutulu learns who orchestrated her father's assassination. Scott makes a promise to her to kill Knox. Down one critical person on the team, Section 20 raids Knox's camp in an attempt to retrieve the triggers.
Stonebridge warns he can't guarantee to regain control over his obsession with wife-killer Craig, but is told he's too invaluable for the team to consider expulsion, especially to balance maverick Scott in duo operations. One of the now assembled warheads is precipitously transported by the client, South Nigerian anti-western rebels, represented by reputable lawyer Christian Lucas, and explodes in a Johannesburg township when arrested by shooting police. Damien still hopes on collaboration with CIA renegade Christy, but is becomes clear she sold out to the terrorists.
Knox turns on his incompetent Nigerian partners, allowing the to be arrested, and even on his own security chief, who protest at abandoning the strong Africa project. Mike gets his confrontation with Craig but spares his life, while a female officer is killed. The nuclear bombs are traced to Cairo, this time for financial blackmail purposes.