The ending has the most intense part of the novel, where Jack and his boys are hunting Ralph down, deliberately trying to kill him.  Before this, the murders of Simon and Piggy were either accidental, or rash actions gone bad.  But now, Jack and his clan have let their more animalistic, violent nature completely take over, and the hunt is on.  As the soldier runs into Ralph on the beach, his questions reflect most of society's attitude about children, that they are only capable of play; that belief is where the irony comes in.  He thinks that they are just playing games; he doesn't expect, nor would he have any reason to suspect, that they are actually trying to kill each other.  He assumes that they are just about "fun and games," and then asks, "What have you been doing?  Having a war or something?"  His question is unintentionally ironic; kids play war, cops and robbers, armies and soldiers all of the time, and his question is referring to that, and it is a gross understatement of the real war that was going on.

The ironic assumption of the pilot emphasizes Golding's point that we are all capable of evil, even small children, if left without guidance, rules, civility, morals, and enforcement of all of them.  I hope that helps a bit; it's a great ending that has a lot of thought-provoking content.  Good luck!