First off, I apologize for not being able to beta-read further than I did, in no small part due to procrastination work, academic commitments, and writing my next mission. So I'll just leave my feelings about this thing here for your convenience, if you don't mind.
While this mission was relatively long by your standards, it was actually a bit easier to follow than I'd expected, especially given two authors and four characters at once. Most missions like this tend to be pretty complex and that leaves a lot of room to get confused and the like, so it's good to see that you two have gone out of your way to keep your agents' personalities distinct. I liked how Will and Chris bounced their dialogue between each other especially, and likewise Ami and VJ, though I was personally hoping for a little more cross-gender dialogue namely with Chris/VJ and Will/Ami. This is a matter of personal taste, though, and I'm still pleased with the final outcome even if I couldn't go through more SPaG stuff than I did. That being said, one thing I felt was a little lacking was that in some places the characters' dialogue seemed to blend together just a little, especially in cases where lines follow each other without indication of who's saying them. I know this is usually because two characters are talking but at the very least it's not a bad idea to distinguish who's speaking a bit more clearly next time. This advice may be hypocritical of me, of course, seeing as I've been guilty of this myself in the past even with some of my solo missions, but it's still worth considering.
The execution of the Sue was a bit surprising, especially given that mind-breaking through poetry is not something I've seen often in previous missions, but it kinda works in this case. I'm assuming the agents were still in their elf disguises, and my guess is that since Elvish music is used to dispel evil in canon, and such a strategy already works for Sue-wraiths, using it to off a straight-up Sue isn't too much of a stretch. Nice touch with Ami's elf form resembling Twilight Princess Zelda, by the way, and I'm reminded now that I need to finish my currently-in-hiatus playthrough of that game as well as actually get more done with the Zelda mission I've been working on recently.
This is a darn good read, all in all, and I do hope you two can collaborate again sometime in the future. Though of course I would recommend picking a shorter badfic next time. XD
As for the fic you're taking on right now, the prospect of agents finding out that the fic they're sporking is actually not as horrible as they feared has quite a bit of precedent, and I myself actually had that happen to me when I sporked that Big Hero 6/Rise of the Guardians crossover last summer. I'd wholeheartedly recommend diplomacy-slash-assimilation if you're far enough into the mission that you can't simply scrap it, especially because it'd be a nice change from simply killing off the OC, and the gods know we could use that more often around here. ;)