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.
The CDC team are forced to work together when another outbreak threatens to overwhelm the Abbey.
Things go from bad to worse on the island. Elsewhere, Walker decides to go to St. Germain after learning about Brother Michael.
Sister Amy makes a power play for control of the Abbey as Alan and Kyle discover a possible cure for the virus.
Alan, Kyle and Winger search the woods for the tree with red sap that might be a cure for the pathogen.
At the abbey, Sister Amy makes a bargain for immortality; and in the woods, the race to find the Bleeding Tree intensifies now that Kyle is infected.
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.
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.
