An Un-Calibrated Centrifuge

Maybe it's because I was tired while reading this one, but I had trouble following the plot. I had trouble following the author's last plot too though. 

 Donner wrote The Deception and The Reunion, and I never quite understood the

I mean, it all came together, but it seemed like a lot of luck.

Just one question under the cut. I might have had more, but I didn't write them down.

At the end, Ax helps one of the free humans on the boat while in his natural Andalite body. The man tells him to "get that alien scum." But how does this guy know that Ax is one of the good guys?

I remembered another one. Jake is against blowing up the Yeerk pool, but not so long ago the Animorphs were all on a mission to do just that. I guess that (failed) mission (/trap) changed his mind about a mass attack on the Yeerk pool? The reasoning sort of makes sense in the book, but we don't get Jake's side of the story so we don't really know why he decides against blowing up the Yeerk pool in this book.