While on a mission in Afghanistan, troop leader Rip Taggart makes a controversial decision. Two years later, Taggart is captured by Boko Haram and his former SEAL Team Six brothers must find and rescue him.

The Seal Team attempts to capture a Boko Haram courier while engaged in a tense raid on an oil tanker in Lagos. They believe the courier could hold information leading to the whereabouts of Rip.

The truth about former group leader Rip's departure from SEAL Team Six comes to light. Trapped in Nigeria, Rip attempts to escape, while the brother of one of his victims in Afghanistan wants revenge.

SEAL Team Six tries to free the kidnapped school girls and their teacher from Boko Haram along with Rip. When they arrive at the camp, the Boko Haram captors are dead and the hostages are gone.

Buckley dies from the wounds he suffered at the compound and the team struggles to deal with his loss; Michael moves the hostages to the site of Muttaqi's recruitment centre in Chad; Rip admits his war crimes on television.

Rip's confession on television ripples through the team; the team raid the home of the owner of the jihadi training centre in Chad; Caulder's adultery comes to light and Bear's marriage becomes strained; Michael angers Muttaqi, who makes a deal.