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.
Chandler and his fractured team join forces with an underground resistance in an attempt to defeat Amy Granderson.
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 to produce and mass distribute the cure.
The crew of Nathan James discovers that hospital ship USNS Solace was sent to sea to wait for Dr. Scott's cure.
With a small group of survivors from Solace in tow, Chandler and his crew square off against an enemy of the most dangerous kind.
Hell bent on avenging the destruction of the labs, Chandler tracks the immunes to Northern Florida. Meanwhile, Rachel comes across a secret formula that her mentor, Dr. Hunter, had been perfecting before the Immunes murdered him.
While XO Slattery struggles to evade the sub in the water, Chandler and the land team infiltrate the Immune compound.
Trying to piece together Dr. Hunter's lost formula, Rachel grapples with the fact Niels, her sworn enemy, is on board Nathan James, while Chandler works to gain intel and reverse the brainwashing Michener suffered at the hands of the Ramseys.
With Dr. Scott on the verge of a breakthrough, Chandler and his team set out to land in search of much needed supplies and materials for her lab.
Rachel is hard at work on a new, more efficient version of the cure while Alisha decodes a message found on a cell phone recovered from the Immunes on land.
Sean Ramsey broadcasts a message implicating the Navy in a disaster. Chandler tries to infiltrate their network and regain the trust of the people. Nathan James locates the source of the signal. Chandler engages in a battle with civilian forces.
Nathan James finds itself trapped between the sub and civilian blockades set up by the Immunes. Chandler sends Dr. Scott and the cure off the ship under the protection of Slattery as the James heads towards its inevitable final showdown.
Nathan James puts a call out to civilians to meet at pre-selected ports across the country, where all will receive the cure. However, small Immune factions remain active in their quest to fight the cure and fulfill Ramsey's dreams.