With nowhere left to turn, a nuclear missile sub Captain and his XO will go on the run and bring their crew to an exotic island. Betrayed, left with no other option but to run, the crew of the USS Colorado will have to fight for its survival.

More than 20 warships close in on the Colorado; as Kendal is forced into a battle on the ground, Prosser questions Marcus' judgement.

Marcus leads a search for three missing crew members of the Colorado, a search that leads them to Serrat's compound, where they receive an ominous demand. Meanwhile, a clandestine meeting between Kylie and Admiral Shepard confirms that the order to fire 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 members of the Colorado and the islanders all together to celebrate their two cultures - a feast in the spirit of Thanksgiving. But the good times turn bad the next morning when an essential crew member is accused of a serious crime. Grace handles the man's defense and is tasked with finding out the truth.

The crew of the Colorado wait for a goodwill visit from their families, a visit that will soon turn into a nightmare as Marcus must consider the unthinkable once again. Meanwhile, the true reason for the nuclear devastation in 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.

In the exciting season finale, a unhappy 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?