For me, Book 41 was the most annoying and unsatisfying book of the series. There didn't appear to be any continuity with the rest of the series, nor any mention of what happened to Jake later in the books. I thought perhaps it was Crayak at first, but there was no characteristic eyeball to announce his presence.
If it were Crayak, I think Jake would have known. I personally (don't shoot me!) think that it was the Orff (or some "real life" version of them, which might have been different than the Orff as depicted in the "future") behind #41. I don't really know why, but they were really the only prominent species in the book aside from the usual ones so I figured they had some importance. They also seemed to be around everywhere in that "future world" - there were Orff in the Yeerk forces, and some in the resistance as well.
The Orff that attack Jake call themselves "the Orff" and not "Orff-Controllers" (and say they're "their own authority," which implies that they're not actually Yeerks per se) and they are never identified as Controllers explicitly, yet there are rebel Orff with the Evolution Front. Maybe Orff like to play Ellimist-style games with the futures of other people. Maybe it's like an MMORPG (MMOrffPG?) for them.
Too much theorizing. That'd be great fanfic material, there.
As for the guy who banished Crayak... I dunno, maybe it was The One. Perhaps The One
is like an equivalent to Father... sort of like a Father-in-Law? Except that when he visits he absorbs everything he can. Maybe he absorbed Crayak in the end and came to our galaxy.
