15 months after the events at Arctic Biosystems, a 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 Brother Michael. Meanwhile, decades in the future, Walker arrives at the same island searching for Alan Farragut. Written by Katie McKinney

A sick child appears while the team is investigating the island, but Sarah suspects something is amiss when the child is miraculously healed; Julia and Caleb make a discovery that furthers the mystery of the island when they dig up Alan's grave. Written by Katie McKinney

It's Day 3 on the island and Seton has disappeared, though not many seem to be too concerned. Kyle talks to one of the children, Lizzie, who tells him Soren had been scared but she didn't know why. Kyle pays a price for trying to get information from the children when, in what seems to be a drug-induced state, they converge on him and give him a beating. Alan wants to know just is in barrels he sees men loading into a barn. While exploring the barn he's knocked out by someone unexpected. Written by garykmcd

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 his brother's secret and gets them both in trouble, meanwhile 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.

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.

Walker and Balleseros arrive at the Abbey while Alan, Kyle and Winger are out in the woods searching for the tree with red sap that might be a cure for the pathogen.

At the Abbey Sister Amy makes a bargain for immortality, while in the woods the race is on to find the Bleeding Tree now that Kyle is infected.

Walker prepares to implant Jordan's baby into Amy while the Navy prepares to implement Plan B, a final solution to ensure the virus and all infected people never leave the island.

While Kyle and Jordan try to escape the island as the followers hunt them, Walker and Alan search for the Mother Tree so that Walker can halt ILARIA's deadly plan.

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.