User blog comment:- Darkchylde/Acnologia's Element?/@comment-173.87.12.242-20141211055642/@comment-4829046-20141214175206

Simple. He couldn't give a damn about the Council. He came to the island, couldn't complete his objective, found some annoying bugs, got bored and then decided to burn them all, left.

And then (in the manga) he returned again when he sensed a big threat to him.