As Alan sets up an isolation unit to quarantine the infected lab workers, Walker and Jordan each face the possibility that they have the deadly virus, too.

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.

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.

Kyle rescues Dr. Sarah Jordan as Alan Farragut fights his own brother, Peter Farragut.