"Alan creates the cure and uses it on Kyle, and asks him to carry a sample of it off the island. Peter is renamed "Eli" and takes control of the abbey. His first order is to eliminate the CDC team. Soren's mother alerts them to the threat. Kyle, Sarah and Soren call in a helicopter to evacuate them, but the attempt is thwarted when Eli opens fire on it. Julia and Alan find that the abbey was built on top of the Mother Tree, and it has sufficient material to carry out the sterilization plan. Alan questions why she is doing it, especially since NARVIK-C may not even exist. They pull guns on each other and as the screen goes black, a shot rings out."
So, Sorens mom got killed... who cares she was a psycho bisatch anyway. Apparently Kyle is going to be his new dad or something. They manage to tell the Navy they have a cure and called for an evac, but Peter/Eli comes out shooting at the helicopter with a machine gun. Meanwhile Julia finds some fungus living in the remains of the "Mother" apple roots. And apparently it is the fungus that causes the sterility all along and not the apples themselves. So now she thinks she can infect all kinds of food items with it.