Chandler (Eric Dane) and his crew head to Guantanamo Bay in hopes of collecting food, medical supplies and fuel, but they come under attack by escaped Gitmo prisoners.

The USS Nathan James faces off against a new foe who demands Chandler hand over Rachel (Rhona Mitra) and her research. When Chandler refuses, he and his crew are put to the test.

Chandler and his crew are put under extreme duress when the ship suffers a catastrophic event and Dr. Scott is in danger of losing all her research on the virus.

Chandler and Slattery (Adam Baldwin) lead a small team into the jungles of Nicaragua on a mission to find monkeys for vaccine trials, but instead run across a former drug kingpin.

Panic spreads throughout the ship when Lt. Danny Green (Travis Van Winkle) comes down with a mysterious illness that could be the virus.

After picking up a distress call, Chandler and a small team stage a rescue, but a surprise attack leaves Chandler and Tex (John Pyper-Ferguson) stranded at sea.

With Chandler and Tex caught in a dangerous situation, Slattery has to step into the role as commanding officer and find a way to rescue them without losing the vaccine prototype.

Rachel and Chandler ask for volunteers to participate in human trials of her vaccine. Meanwhile, Chandler's wife and father do everything they can to keep their family alive.

Chandler and his crew finally return home in the season finale, but he discovers something absolutely terrifying about this brave new world.