Yes! It's in Ch. 5 of #46, during the discussion of whether to steal humans' identities (thereby getting said humans court-martialed) in the name of trying to stop a nuclear war. From p. 25:

“I’m not denying it,” Marco said coldly. “But Jake’s right. Things have changed. We can’t be asking anymore whether something’s right or wrong. We really need to start asking whether it’s expedient.” [...] Jake took Cassie’s hands in his own. I noticed Tobias turn slightly away. “Cassie, I’d never ask you to do something you don’t want to,” Jake said softly. “Or can’t. But here’s the thing. I think our assumptions are right. I think Visser One is about to launch open war. Entire cities might be incinerated. Whole countries. Maybe, just maybe, if we strike now, if we do everything we possibly can, maybe we can keep that form happening.” He smiled sadly. “I’m not sure I could live with myself if we didn’t do all that we could.” Billions of lives weighed against the ethics of six “kids…” “And I’m not sure I could live with myself if we did,” Cassie answered softly. “Jake, there’s always a reason to abandon morality. We’ve been through this so many times. Someone’s always saying, ‘forget about right or wrong, we’ve got to win.’” “I know, I know.” Jake squeezed Cassie’s hands. “But…doesn’t it always come down to each one of us, all alone, asking ourselves: Am I right in doing whatever it takes for the greater good? And, do I trust myself enough to know I won’t become evil in the process? It always comes down to something that personal.” Or the situation, I thought. Or the special circumstances. A morality of convenience. Not unlike Andalite morality….

One of my favorite passages, in one of my favorite books. The later Ax books are, IMHO, diamonds in the rough when the series starts to get uneven. They tend to be where we get the most open discussion of ethics in the series. And Ax's insistence on neutrality makes him one of the most interesting narrators in those sequences — he sees that Marco is right that there's not time for debate. He sees that Cassie is right about how easy (and dangerous) it is to abandon ethical principles for expedience. He understands Jake's point of view about needing to keep themselves. Heck, he even notices (though no one else does) how much it will always bother Tobias that Jake and Cassie get to have such effortless physical affection with each other.

But they are also intentionally uncomfortable. Moreso than the early series, even. The kids have to make desperate, horrible choices as the war becomes more open (such as the human morphs without permission and Ax and the nuke here). As a kid it was a lot.

I wondered before the reread if maybe it was because when I first read through I was getting to an age where I could better understand the darker elements of the books around this time that I didn't notice before. On the reread, though? I think it's just that the stakes escalate so much once Esplin is promoted to Visser One that the protagonists end up fast-tracked into their endgame spiral in a way that crept slower before. It's the shift to open war that moves their character arcs into hyperdrive and the choices get darker and weightier by the same measure.