Peter and Sarah lead a CDC team in investigating a terrifying new outbreak on board a boat, which leads them to an island inhabited by a religious cult isolated from the outside world. Elsewhere, Julia Walker arrives on the island with her own agenda and is taken captive by a stranger.
Sarah discovers Alan's presence on the island, but he refuses to divulge what it is he is doing there. Brother Michael allows the CDC team to begin investigating the illness after a child is infected. In the future, Julia determines to dig up the newly-discovered grave.
Jordan and Peter go in search of lost samples and discover a danger in the forest, while Sister Amy uses the children to plots against Kyle and the team. Alan makes a discovery, and in the future Hiroshi captures his daughter and tries to get answers.
While Michael struggles to keep his followers in the abbey under control Sarah continues to investigate Soren's disappearance, and Alan grows suspicious of his brother. In the future, Walker attempts to escape from her delusional father.
Peter reveals his brother's identity to Michael, landing them both in a predicament. Kyle identifies the island's honeybees as the source of the infection's spread, while Sarah fights for her life. In the future, Julia is rescued and nursed back to health.
Michael's plans to continue his line leads to a new outbreak throughout the abbey, forcing Kyle to work with Alan. Off the island, Julia decides to act when her peers at Ilaria decide to unleash the Narvic virus on the global population.
Sarah awakens in a mostly abandoned building, fearful of what has been done to her. While Alan's memories begin to return, Peter finds that he has a new cellmate. Elsewhere Walker decides to set out for St. Germain, and Brother Michael takes drastic action to secure his increasingly tenuous position.
In the wake of Michael's terrible culling Sister Amy makes a power play, while a military team arrives on the island with news that the virus has spread beyond the island. Meanwhile, Sarah reveals a secret to Kyle.
Sister Amy consolidates her power, attempting to force Sarah to help her gain immortality. Outside the abbey walls Alan and Kyle join Lt. Commander Winger's team to search for a potential cure for the pathogen, and Walker and Balleseros arrive on the island.
The search for the Bleeding Tree intensifies as Kyle becomes increasingly symptomatic. Sister Anne leads Peter on a journey that reveals the abbey's darkest secret, and Sarah and Julia team up to try and give Amy what she wants.
Alan and Winger return to the abbey with hope of a potential cure, only to learn that the Navy is about to attack the island with an extinction protocol. Peter is convinced to take drastic actions, and Walker gives Sister Amy a new plan.
The new leader of the abbey calls for the death of the CDC team, prompting Kyle and Sarah to try and flee the island. Julia and Alan attempt to find the Mother Tree in the hopes of stopping Ilaria's plans for genocide.
Alan and Julia clash over whether to hand over the Mother fungus to Ilaria, while a horribly disfigured Amy confronts her mother. Peter enacts his endgame, and in the future Julia learns the true identity of her island companion.
