The Yeerks are finally starting to realize that the ”Andalite bandits” are probably not aliens at all. They're finally starting to realize that maybe they've been dealing with humans all along. And no one-especially the newly appointed Visser One-is happy with this knowledge. Not happy at all.
When Tobias, the other Animorphs, and Ax realize that the Yeerks are about to find them, it's by accident. But that doesn't make the discovery any less serious. Because in a war, one side wins. And one side loses.