It has been 73 years since Alex failed and the Humans lost the Cyborg Wars. Since then, the Humans have been enslaved. Scientists have developed a new DNA strain, which could signal the end of the Cyborgs, and they inject it into a volunteer. When the Cyborgs learn of the woman and the baby they list both for termination. To escape, she takes a stolen Cyborg ship and transports back in time to East Africa in 1980, where the mother is killed, but the baby is saved. It takes 20 years, but the Cyborg bounty hunter Nebula finally locates the girl, named Alex, and travels back in time to terminate her.

Young Jim Hawkins, while running the Benbow Inn with his mother, meets Captain Billy Bones, who dies at the inn while it is besieged by buccaneers led by Blind Pew. Jim and his mother fight off the attackers and discover Billy Bones' treasure map for which the buccaneers had come. Jim agrees to sail on the Hispaniola with Squire Trelawney and Dr. Livesey to find the treasure on a mysterious island. Upon arriving at the island, ship's cook and scalawag Long John Silver leads a mutiny of crew members who want the treasure for themselves. Jim helps the Squire and Hispaniola officers to survive the mutiny and fight back against Silver's men, who have taken over the Hispaniola.

The last witch hunter is all that stands between humanity and the combined forces of the most horrifying witches in history.