The crew members arrive at the Guantanamo Bay military base to collect food, fuel and medical supplies. When they come under attack by escaped Gitmo prisoners, they team up with a gruff private contractor to push back against the offensive.

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 the horrifying revelations and reversals of fortune in Baltimore, Chandler and his fractured team join forces with an underground resistance in an attempt to defeat Amy Granderson. With doses of the cure running low, Rachel tries to do some good for the sick while remaining a prisoner at Avocet. Meanwhile, Slattery and the crew of Nathan James are in a race against time to save an injured Dr. Tophet and regain control of their ship.

After the horrifying revelations and reversals of fortune in Baltimore, Chandler and his fractured team join forces with an underground resistance in an attempt to defeat Amy Granderson. With doses of the cure running low, Rachel tries to do some good for the sick while remaining a prisoner at Avocet. Meanwhile, Slattery and the crew of Nathan James are in a race against time to save an injured Dr. Tophet and regain control of their ship.

Nathan James returns home to Norfolk on a mission. With his family now safely aboard the James, Chandler sends his crew in search of their friends and loved ones.

Still trying to piece together Dr. Hunter's lost formula, Rachel grapples with her sworn enemy's presence on board the Nathan James.

Chandler must find a way to return to his old crew and investigate a dangerous new foe.