15 months after the events at Arctic Biosystems, new CDC team with the addition of biotoxicologist Kyle Sommer respond to a potential outbreak on a Windjammer in the Northern Pacific. Their search leads them to an island occupied by a mysterious cult led by the charismatic Michael. Meanwhile, 30 years in the future, Walker arrives at the same island searching for Alan Farragut.

The CDC team continue to investigate the island; at the same time, they discover Peter's brother, Alan, is a member of Brother Michael's cult, and his warnings for them to leave the abbey fall on deaf ears.

Peter and Jordan leave the safety of the Abbey to retrieve some specimens and discover just what’s living in the woods, meanwhile Sister Amy plots to make them leave forever.

As Michael struggles to keep the abbey under control, the CDC team moves closer toward tracking the source of the pathogen. Alan fights the urge to rejoin his team and confronts the reality about Peter’s allegiances. In the future, Walker makes a desperate attempt to escape from her delusional father, with potentially deadly consequences.

Michael locks Peter and Alan in a pit. Alan escapes and discovers that Kyle has a secret of his own. Agnes reveals a shocking truth to Michael, who drastically turns on her for doubting him. In the future, Caleb uncovers Walker's deception and takes matters into his own hands.

Amy creates an outbreak of the disease. Michael torments Peter in the pit. Alan, Jordan and Kyle discover the truth about the Abbey's food chain. An uprising at the Abbey threatens the safety of the uninfected. In present-day Paris, Balleseros meet an unlikely immortal.

As Peter gains a new cellmate, Michael takes extreme action when his followers begin to mutiny.

The Coast Guard arrives on the island to take the CDC team to another island to deal with another outbreak of the pathogen. Meanwhile, Sister Amy has to contend with Brother Michael and his plans.

Alan, Kyle and Winger search the woods for the tree with red sap that might be a cure for the pathogen.

The Abbey becomes a house of horrors as Kyle struggles with his infection and Anne begins to shape a successor to Michael.

The Navy prepare to implement Plan B, a final solution to ensure that the virus and everyone infected with it never make it off the island.

The uninfected are hiding in a secret bunker on the base as the CDC attempt to retrieve the canisters with the virus and the cure while the Ilaria assassins capture Hatake and force him to chose between which one of his children they will kill first.