Is the fire in Chapter 12 of Lord of the Flies at all related to the story of the flood in the Bible?
The connection would be that in both the flood and the fire, all the people would have been killed except that the survivors were saved by an outside force. That's a rather tenuous connection because the differences outweigh the similarities.
In the Bible, the flood was a sign of God's judgement against the people living at the time. It was started and ended by God. In "Lord of the Flies", the fire is actually started by the boys themselves in order to smoke out Ralph. In the Bible, God warns one family of the coming of the fire and they built an ark in order to survive. In "Lord of the Flies", Ralph has no "ark" and is about to be killed except for the British Navy. It's true the navy comes on a boat, just as Noah is saved through the ark. But Ralph escapes the fire; Noah survives the flood inside the ark.
Finally, Ralph is saved but so are all the other boys. In the flood, all mankind, except for Noah's family, were destroyed. So, one could make an argument that the two are related, but the relationship between the two incidents is rather weak.