John Porter resigns from the SAS following the aftermath of a rescue mission in Iraq on the eve of the American led invasion in 2003, where two fellow soldiers were killed, apparently by a thirteen-year boy Porter had failed to kill, leaving him responsible. Seven years later, Porter is "reactivated" following the kidnap of journalist Katie Dartmouth by the same terrorists he fought seven years ago, including the same boy: As'ad.

Porter is captured by a Pakistani terrorist called Latif while investigating a planned operation of Latif, Project Dawn. Sergeant Michael Stonebridge finds disgraced ex-Delta Force operative Damian Scott, who would not be hired by even private military contractors, who previously worked with Porter to track Latif. After Porter is executed, Section 20 discover Porter left the team clues to a hotel in New Delhi, India, where a group of terrorists attempt to capture a weapons scientist with knowledge of hidden weapons of mass destruction originally used to plant in Iraq, which serves as a part of Project Dawn. The weapon, namely VX nerve gas was kept in storage, and Latif has known about its existence.

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, 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 for murdering his wife, and Scott has to contend with Central Intelligence Agency (CIA) agent Christy Bryant, 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 fulfills his revenge, and Knox kills himself when he fails.

Scott and Stonebridge are recalled from holiday in California to capture Leo Kamali, a high ranking member of a terrorist cell led by al-Zuhari, an elusive terrorist. After capturing him in Colombia it is revealed that Kamali is working deep cover with the CIA to stop al-Zuhari. As Kamali is pressured to work with Section 20, Dalton is suspended by Colonel Philip Locke, who takes charge. Dalton is later killed by the Real Irish Republican Army (IRA), who have joined forces with al-Zuhari's group. In the meantime, Scott and Stonebridge are wanted by the Russian mafia after killing the son of mob boss Arkady Ulyanov in Colombia.

From the tropical beaches of Thailand to the towering peaks of the Swiss Alps, Strike Back: Legacy thrusts Section 20 onto a mission the scale of which has never been seen before as this season Scott & Stonebridge go up against the state sanctioned criminal wing of the North Korean regime, known as Office 39. Coordinated by a beautiful and devoted North Korean agent deeply embedded in the British Establishment, Han Li-na is secretly assembling intercontinental ballistic missiles capable of wiping out Washington and London. Putting a stop to the threat posed by North Korea becomes Section 20’s undoing when, in a bid to ease escalating global tensions, Sir Charles Ridley a senior figure within Whitehall, brokers a deal with North Korea to eliminate Section 20.

Tasked with covert military intelligence and high-risk operations, the resurrected unit, known as Section 20, embarks on a lethal manhunt that will uncover a vast web of interconnected criminal activity. As the team journey across the Middle East and Europe, they uncover a deadly conspiracy which threatens to overwhelm them all and change the face of modern warfare forever.

When a Russian bomber crashes in the South China Sea, the covert special-ops soldiers of Section 20— Thomas “Mac” McAllister, Samuel Wyatt and Gracie Novin — are sent to investigate. There, they cross paths with Katrina Zarkova, a rogue Russian operative with questionable loyalties. Under orders of the new commanding officer, Col. Alexander Coltrane, Section 20 pursues stolen contents of the Russian jet across Southeast Asia. They will work alongside the Malaysian police to shut down a Triad gang in Kuala Lumpur, uncover a corrupt plot by a wealthy Indian businesswoman running for Parliament and plunge into the jungles of the Golden Triangle in Myanmar, facing off against mercenary drug agents and terrifying warlords as they uncover a conspiracy that threatens to push the world to the brink of global conflict.

The members of Section 20 are thrown back into combat when a seemingly-straightforward mission in Kosovo to rescue a British scientist uncovers a conspiracy.