"Alan starts analyzing the red sap and Soren's blood, in hopes of finding a cure. Peter declares that nobody will leave the island, especially Alan. Julia and Sarah begin the procedure on Amy, who wakes up with the silvery eyes of an immortal. The Navy implements "Plan B", and sprays the island with an agent that kills on contact. This apparently eliminates the Coast Guard crew as well as damaging Mother. Amy quickly finds that she has been tricked."
So they tricked Amy into thinking they had made her an immortal, so she ran outside during the poison spraying and becomes disfigured. Then somebody dragged her away at the end, I'm figuring that it was her lover/brother Landry who is now also disfigured. Now they can be monster parents raising a whole new group of inbred monster kids. Don't understand how she survived the poison since it killed every other thing on the island, even the root that was shut up in a box. That spray sure killed that monkey super fast, guess they just wanted her to survive as a mutant.
Peter is still running around killing people for no apparent reason other than he's having a power trip and thinks he can take Michaels place. The Coast guard people are all dead and now Alan and his people still need a way off the island with the cure.