The third series consists of ten episodes. Former military intelligence operative, Major Rachel Dalton takes charge of Section 20. They work throughout Africa to gain their hands on four nuclear triggers which are in the wrong hands after a mission in Somalia. The triggers have originally been sold to Conrad Knox (Charles Dance), an English billionaire and philanthropist based in South Africa, who runs the Knox Foundation, charged with disarming unstable regions. However, it becomes apparent that he is using the weapons to arm his own militia, and is using the triggers to build nuclear weapons with the intent on liberating Africa "to a point where its voice is not just heard but listened to." Due to Knox's influence, Section 20 is forced to go dark to stop him. In the meantime Stonebridge seeks revenge on Craig Hanson (Shane Taylor) for murdering his wife, and Scott has to contend with Central Intelligence Agency (CIA) agent Christy Bryant (Stephanie Vogt), whom he used to work contract killings with. By the conclusion of the series, two of the bombs are recovered, and the remaining two were disarmed before they could destroy Johannesburg, Stonebridge fulfils his revenge, and Knox kills himself when he fails.
Scott is ordered to the Kenyan desert to secure the transfer of Keemal, a Libyan functionary seeking asylum, to British Embassy officials. Instead, Scott ends up in the midst of a kidnapping plot that takes him and three hostages to war-ravaged Mogadishu--and into the clutches of a brutal local warlord named Huseyin Waabri. As his friend risks life and limb in Africa, Stonebridge is back in the United Kingdom training Section 20 recruits--a job that takes a perilous twist when an unstable soldier named Jake Hanson, whose brother Craig once served with Stonebridge, cracks.
Surprised to discover that a Waabri hostage named Rachel Dalton is in fact a top-ranking military intelligence operative, Scott, now accompanied by Stonebridge and Richmond, staves off a hostile onslaught in Mogadishu by Waabri and his sexy associate Asmara, who are hoping to start a new life by selling four nuclear triggers to a mysterious buyer in South Africa. When the team returns to London, Section 20 gets a new leader to replace Colonel Grant, and Stonebridge reconciles with Kerry, albeit briefly.
After a personal tragedy, Stonebridge applies for a transfer back to Section 20. While the team remains concerned about his mental state, Scott encourages them to allow Stonebridge back into the unit.
Tracking the missing nuclear triggers to Niger, the team believes that a radical religious leader may have malicious plans to use or sell them. They raid a compound in Niamey and discover another party with interest in the region and ties to Scott’s past. Believing that courier Othmani (Said Taghmaoui) has the triggers, they track him as he tries to leave Niger through the northern desert, where he is captured by a nomadic group led by Markunda (Laetitia Eido). Stonebridge and Scott are airdropped into the desert to negotiate.
Holed up with Markunda and a wounded Othmani in a remote Algerian farmhouse, Scott and Stonebridge prepare for an inevitable assault by the forces of El Soldat, who seeks to take possession of the triggers and his half brother. At the Section 20 crib, Sinclair queries Dalton about her relationship with Othmani; the Major in turn calls Othmani to question his blind allegiance to a duplicitous scoundrel. A bloody firefight breaks out as dawn arrives, but the victory--and the nuclear triggers--end up in unexpected hands.
After stealing the nuclear triggers from Stonebridge (Philip Winchester) and Scott (Sullivan Stapleton) in remote Algeria, Knox’s (Charles Dance) task man Karl Matlock (Vincent Regan) and sniper Jessica Kohl (Natalie Becker) resurface in a seemingly unrelated Capetown kidnapping. Section 20 discovers interesting information about Peter Evans (Paul Freeman), the victim’s father, who has mysteriously flown to Capetown. A new third party interferes with the mission and both Scott and Stonebridge make costly mistakes.
Stonebridge and Scott confide in each other about their mistakes – Stonebridge’s desire for revenge on Craig Hanson (Shane Taylor), who has appeared in Capetown, and Scott’s connection with Rebecca (Lyne Renée), a Mossad agent tracking their case, but with very different orders from theirs. Knox takes Evans to a secret facility, where he reveals how he plans to make Africa a world power. Stonebridge befriends Knox’s idealistic daughter, Ava (Olivia Grant), who runs their foundation and weapons decommissioning program.
Now working covertly without South African government permission and with limited resources, the team looks for a reason Knox would break opposition political leader Walter Lutulu (Eamonn Walker) out of a Zimbabwe prison. They try to track him through his respected activist daughter, Lilian (Tracy Ifeachor), as authorities from the currentpolitical regime also look for her. A familiar face offers his unique skills to Knox, who uses his government influence to apply pressure to Section 20.
Fueled by the Lutulu shooting, community unrest continues to spread through South Africa and north to Zimbabwe. Trapped in an isolated police station, Stonebridge questions the shooter and looks for a safe escape. Scott and Lilian take her father to the hospital and are pursued by other assassins. Knox and a surprise ally discuss a new plan.
Now a wanted man, Knox (Charles Dance) hatches a plan for the nuclear bombs that involves several African nations plagued by political unrest and unstable militia factions. When the transport for one of the nukes is recognized at the scene of a crime, Stonebridge (Philip Winchester) and Scott (Sullivan Stapleton) mount a dangerous pursuit. Dalton (Rhona Mitra) confronts Christy Bryant (Stephanie Vogt) about the CIA’s dealings in Africa. Matlock (Vincent Regan) reveals his true motives behind joining Knox to Hanson (Shane Taylor), who continues to be a major distraction for Stonebridge.
Scott questions Bryant about her role in Knox’s plan and appeals to her for help, but Scott’s dark past may dictate his course of action. Stonebridge attempts to focus on the mission, but is consumed by thoughts of revenge. South Africanpolice team up with Section 20 to find the nukes and Knox before he can carry out his plan.