I'm willing to bet that Ix and Charlotte weren't even at the halfway point of the badfic before they decided to do the Duty. Am I in the ballpark?

As for the usual SOH post-mission usual fare:
1) “This is why establishing the setting is important, people,” Charlotte said through gritted teeth. “Also, can we charge for showing thought-speech as bolded italics?”
Actually, that shouldn't be a charge. Unless things have changed on FFN, they actually have a problem with chevrons. An unfinished Animorphs goodfic that I ran across (the very first FFN fic that I ever read, IIRC), ran into this issue the hard way.

2) The chapter ended with the Animorphs agreeing that Ax and Tobias would watch the Sue, and the agents were thrown into the next, landing in the yard outside her house.
The next what? Obviously the answer is "chapter", but it takes a few moments' thought to figure that out. Please consider being a bit more specific; it only requires adding one more word.

3) So they followed the canons and Sue until they found the entrance to the Yeerk Pool inside the employees only room, though Ax was a bit too distracted by the Sue’s beauty to think about such silly things.
"employees only" should be hyphenated.

I'm still holding out for an appropriately god-awful crossover, preferably involving Ax or other Andalites, in case anybody happens to see one. The best I've got right now is this, which is maybe better MST material than mission material. The author's notes almost outweigh the story, if you can call it that. O.o

(Making Ilraen and Farilan MST it could be fun, though, come to think of it...)

Anyway, the mission! I enjoyed it, and I'm interested in this new take on fixing the problem of Ix and Lottie's different lifespans. Charlotte researching ways to de-vamp herself from various continua could be a fun exploration of different takes on the vampire myth, but even not getting into it in detail, it still provides some food for thought. It also shows how devoted she is to being with Ix, which is a great bit of characterization.

Speaking of showing over telling, the mission did a good job of highlighting how the Sue failed at it with regards to her angsting about her lack of friends while at the same time behaving in an obnoxiously standoffish way. And wow, the speshulness. Jeez. Good riddance to her.

I did have one moment of confusion here:

Ax and Tobias retreated to the bathrooms to morph cockroaches, and just as they were making their way back to the pool entrance, the scene changed again, dumping the agents behind the stack of hay bales.

It took me a minute to figure out that the scene had changed back to Cassie's barn rather than something new, so I struggled a bit trying to make sense of hay bales in a Yeerk pool, where I'd have expected the story to go next. Y'know, if the fic had actually bothered itself with detailing an important action like scouting enemy territory. {= P This could be easily fixed by the addition of a few words, either "the scene changed again back to Cassie's barn" or "behind the stack of hay bales in Cassie's barn." (Not both, of course.)

I feel bad for Lottie at the end. Unbridled hope and enthusiasm meets the cold steel wall of elitism and xenophobia. Ouch. Good to know Ilraen has been seeing her nice side so far. Guess he's in for a rude awakening when he finds out just how much work he has cut out for him.

~Neshomeh

Read this mission while waiting for the lecturer to get into something interesting, no siree.

The Good: I like the characterisation of Ix and Lottie. There is no Talking Heads, which is nice. The mission is... I'm not sure how to say it, but it was an easy, flowing read.
The Bad: there's a distinct lack of funny in the mission. Might just be me, though.
The Ugly: the Sue, who else?