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.

As the CDC team reels from the devastation at the Abbey, the Coast Guard arrives with news of a new outbreak. Meanwhile, incensed from her imprisonment, Amy takes control of the Abbey, locking Michael in the pit. Jordan, convinced her baby still lives, reveals the truth of the immortals to Kyle in exchange for his help. In the future, Walker's quest for Hatake's missing sword causes her to delve deeper into the Abbey's secrets

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.

Plan B are determined to make sure that the virus and the infected people do not leave the island.

Peter finds his purpose as the new leader of Michael's order as the CDC team continues the desperate search for the Mother Tree.

Alan's relationship with Walker reaches a bloody climax, while his sibling feud with Peter erupts in flames. Elsewhere, Kyle does his best to protect a possible cure for the mycosis.