The submarine "USS Colorado" receives orders to fire nuclear weapons at Pakistan. When the Captain and XO demand confirmation, the Colorado crew are declared rogue enemies of their own country.
More than 20 warships close in on the Colorado. As Kendal is forced into a battle on the ground, Prosser questions Marcus' judgement.
A search for missing crew members leads to Serrat's compound and an ominous demand. A clandestine meeting between Kylie and Admiral Shepard confirms that the fire order came through a back channel.
Even as Marcus and Sam learn that they have been charged with treason against the United States, a greater threat within their own crew is brewing. Meanwhile, an old friend of Sam's, Paul Wells, pays Christine a visit and tries to ease her fears about her husband.
In an attempt to end the standoff on Sainte Marina, Marcus and Sam enter into tense negotiations with the U.S. Government. Meanwhile, when a critical system fails, Grace must take command of the Colorado on a perilous repair operation.
The crew is hit with an attack by an unknown force unlike anything they’ve seen before. As confusion and aggression take hold, Marcus and Sam can no longer trust their own senses even as they race to save the sub and defend the island.
As Marcus and Sam hunt for the traitor in their ranks who stole their nuclear launch key, Prosser disobeys orders and starts a small war he can’t control. Meanwhile Grace and James must work together to defuse a dangerous situation, as back in D.C. Christine is indicted as Sam's co-conspirator.
Marcus brings the islanders and the members of the Colorado together for a feast in the spirit of Thanksgiving; Grace searches for the truth when an essential crew member is accused of a crime.
The crew waits for a visit from its families; Marcus must contemplate the unthinkable; the reason for the attack on Pakistan is revealed.
Sam and James depart the island in a daring rescue attempt. Back on the island of Sainte Marina, a Chinese diplomat arrives to make a deal with Marcus. With scarcity and a prison problem plaguing him, Marcus finds himself treading down a more treacherous path than he could have imagined.
A typhoon, a mutiny and a Washington coup d'etat will force Marcus and his crew into unlikely alliances. As Sam's grief strains his loyalty to Marcus, will Sainte Marina get the supplies it so desperately needs? How far will Marcus go to ensure the crew's survival -- will it cost him his life?
Kylie works with Admiral Shepard to bring down the President, using evidence of what really happened in Pakistan. This affords Marcus the opportunity to surrender the Colorado, if all goes according to plan. Meanwhile, Speaker of the House Conrad Buell, meets with a small group of Washington heavyweights to discuss the unthinkable when Kylie’s video information helps persuade him to participate in a risky and treasonous maneuver.
In the exciting series finale, a violent battle for control erupts on the submarine, which leaves the Colorado vulnerable to capture by a third party — one with an exploitative plan. Can Marcus and Sam take control of the sub before it’s too late?
