A global virus pandemic nearly obliterates the earth's population, forcing the crew of a naval destroyer to confront the reality of their new existence in a dangerous new world where they are among the only survivors. They must find a way to pull humanity from the brink of extinction.

Chandler and his crew head to the U.S. military base in Guantanamo Bay in search of food, medical supplies and fuel; escaped prisoners attack the search teams; the teams enlist the help of a private contractor.

The James faces off against a new foe who demands Chandler hand over Rachel and her research. When Chandler refuses, he and his crew are put to the test as Chandler engages in a series of risky strategic moves. But it turns out their new enemy has his own horse in the race to find a cure for the virus.

Days after a trying series of events at Gitmo, Chandler and his crew are put under extreme duress when the ship's propulsion system suffers a catastrophic event. With Dr. Scott in danger of losing all her research on the virus and a crew overworked, overtired and desperately low on drinking water, Chandler’s leadership and ingenuity are put to the test.

With Rachel close to a breakthrough on her vaccine, she, Chandler and XO Slattery lead a small team into the jungles of Nicaragua on a mission to find monkeys for her vaccine trials. While there, they find much more than they bargained for when they run across a former drug kingpin who will stop at nothing to maintain his stranglehold on his oppressed society. Chandler and his men find themselves in a huge moral dilemma over whether to eliminate this menace or take what they need and continue on with their mission.

After returning from the horrors of Nicaragua, panic begins to spread throughout the ship when Lt. Danny Green comes down with a mysterious illness that could be the virus. Losing faith in Rachel and her failing vaccine trials, Chandler now has to deal with a restive crew. If he fails to keep the crew together, the whole mission is in jeopardy.

After picking up a distress call near Jamaica, Chandler and a small team stage a rescue attempt. But a surprise attack leave Chandler and Tex stranded at sea. Slattery and the crew search desperately to find their lost at sea Captain and his comrade, hoping to do so before their enemies beat them to it.

With Chandler and Tex caught in a dangerous situation, Slattery has to step into the role as commanding officer. Torn between a mission with the fate of the world at stake and a Captain (and friend) in danger, Slattery has to find a way to get his people back without losing the most important asset: the vaccine prototype.

Rachel and Chandler ask for six volunteers to participate in human trials of her vaccine, but the tests could be a living hell as the virus and the vaccine do battle inside their bodies. Meanwhile back in the States, Chandler’s wife and father are doing everything they can to keep their family alive.

In the season finale, Chandler and his crew finally return home, where a former D.C. power player is fending off a dangerous warlord who threatens her hopes of restoring law and order in society. Now with a location and a means to finalize their mission, Chandler sets out to save his dying family, only to discover something absolutely terrifying about this brave new world.