The show is about the renegade crew of a United States Navy Ohio-class ballistic missile submarine, the fictional USS Colorado (SSBN-753), that receives an order to launch nuclear missiles at Pakistan, through a backup communications channel. When Captain Marcus Chaplin (Andre Braugher) asks for confirmation via official channels, he is relieved of command. His second in command, Lt. Commander Sam Kendal (Scott Speedman), also questions the orders and the vessel is fired upon by the USS Illinois, killing crew members of the Colorado.
Realizing that they have been declared enemies of their own country, they set up camp on the island of Sainte Marina (a fictional island located in the Indian Ocean), commandeer a NATO communications facility, and declare a 200 mile exclusion zone around the island. When B-1 Lancer bombers are sent to attack the submarine, Captain Chaplin launches a nuclear missile towards the US to impress upon them that he is serious.
At the same time, the crew must find a way to prove their innocence and find out who set them up so that they can return home.