They are going to have a Jacob episode in the future which shows how he got on the island. Some people have said on the set they were wearing Roman Costumes.
So I am thinking, it could be the Anti-Christ.
Jacob was chosen to take the Anti-Christ on a remote Island and keep that evil bottled up there.
In actual, the theory is that the anti-christ is on a remote island somewhere and when the day of judgment nears he will break his chains and come to the world.