In the series premiere episode, Captain Tom Chandler and the crew of the USS Nathan James set out for the Arctic with two civilian virologists, Dr. Rachel Scott and Dr. Quincy Tophet (Sam Spruell), who claim to be studying birds. When they come under attack by a renegade team of Russian forces, Chandler learns these virologists are actually collecting samples of the source of a deadly virus that has wiped out over half the human population while they've been at sea. As they head home on the orders of the remaining U.S. government, Chandler and his crew realize that home is a shadow of what they left, and the safest place to develop a vaccine for this deadly disease is out at sea on their ship.

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.

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 (series star Travis Van Winkle) 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.