In the second-season premiere, Drs. Peter Farragut and Sarah Jordan are joined by Kyle Sommer when they battle a new deadly virus on a mysterious wooded island.
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.
Jordan and Peter travel outside the safety of the abbey to retrieve some specimens and discover just what's living in the woods; at the same time, Sister Amy plots to make the CDC team leave forever.
Michael struggles to keep the abbey under control as the CDC team move closer toward tracking the source of the pathogen; at the same time, Alan fights the urge to rejoin his former colleagues and comes to terms with the reality about Peter's allegiances. In the future, Walker takes a risk attempting to escape her delusional father.
Peter reveals is brother's secret and gets them both in trouble; at the same time, Kyle has his hands full trying to quarantine the orchard and the infected hive.
Kyle and Jordan attempt to flee the island, but their escape is made more difficult by the followers who are hunting them down; Walker and Alan plan to halt ILARIA's deadly plan as soon as they find the Mother Tree.
In the Season 2 finale, 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.
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