Season Two begins with a cure for the Red Virus and the goal to save the human race. Navy Captain Tom Chandler and his crew return to the States unsure of what they will find. As the crew seeks to find survivors and their families, they encounter a new, emerging enemy who’s vying for control and may hinder the mass production of the cure.
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.
The crew of Nathan James discovers that hospital ship USNS Solace was sent to sea to wait for Dr. Scott's cure. Captain Chandler sees an opportunity to add another ship to their fleet while Rachel is eager to find a lab better equipped to replicate the vaccine. When Solace fails to respond to radio communications, Chandler and his team board the ship...and come face-to-face with an unexpected enemy.
With a small group of survivors from Solace in tow, Chandler and his crew square off against an enemy of the most dangerous kind - a nuclear-powered submarine led by rogue British naval officers, Sean and Ned Ramsey. XO Slattery interrogates a captured mercenary from the hospital ship in an effort to extract information on the sub and its mission. As Nathan James engages in a perilous game of cat-and- mouse, the truth about the mercenary sub unfolds.
After a message is broadcast implicating the Navy in a devastating disaster, Chandler looks to infiltrate the network and regain the trust of the American people.
With their mission now fully dedicated to spreading the cure, Nathan James puts a call out to civilians to meet at pre-selected ports across the country.