Recently I started a crossover fanfiction based on the premise of Godzilla getting teleported to the RWBY universe. If you read the synopsis, you can see my original intentions for the story: Godzilla gets transported, people do shit to him, he gets high on Dust, chaos ensues. Once you read the prologue (the only part that's been posted, at the time of this writing), you can already see where I derailed my whole premise: a second monster and a human being have also been teleported, and from looking at the synopsis they apparently have nothing to do with the rest of the story. This is a problem for properly integrating them, and I'll talk about how situations like this can be avoided entirely, and possible solutions once you've gotten yourself into it.
First, you may think avoiding this might be quite easy: just plan your story better next time. The problem with this is that a scene often sounds better in your head before you actually commit it to paper. Godzilla was originally just going to wander into Tokyo and get blasted by Dimension Tide; hell, in one draft it was just going to be a straight continuation of Godzilla vs Megaguirus. The problem is that while a low-key scene like that might work okay in a first chapter, a prologue calls far a more intense scene which leads you into the story proper. No matter how you look at it, Godzilla wandering around and suddenly disappearing is pretty damned hard to make sound interesting. Looks good in the mind's eye, but it's not very compelling in writing. Godzilla needed a sparring partner, and I couldn't have realized that until I started writing.
The second way to avoid this is to run the idea by someone else. This is fairly foolproof most of the time, and is the strategy I'd recommend. The only reason I didn't do this is because the people I could talk to either aren't interested in this type of story, or were not easy to reach at the time.
Lastly, you can page-vomit some ideas before you actually plan the whole story. It lets you see which premise is the most workable, allowing you to proceed from there. This is really what I should have done, and I just kind of didn't. Hey, it's the first time in like 5 years I've actually tried to write, cut me some slack!
As far as fixing this, there are a few things I could do. The first would be to have Emi team up with the main cast somehow to defeat Godzilla. However, the story would last all of maybe two chapters if I did that, plus the RWBY characters would get shoved into the background while the entire focus is on Emi and Godzilla; I might as well set this story in Equestria for all the significance it would have as a crossover setting. Considering this story was intended to last between 10 and 20 chapters, this is clearly not an acceptable option.
Option two would be to kill off Emi and Ghidorah. This would allow the story to proceed on-track with no further alterations, and save me several headaches. Again, this has problems: Emi and Ghidorah have already been established as characters we somewhat sympathize with, and having them basically die offscreen has the potential to put a bad taste in readers' mouths as they progress through the story. It could be seen as wasted potential, and that would distract from how the story actually unfolds.
Option three is to draw further inspiration from Godzilla Neo and have Ghidorah possess Emi, making her an antagonist from this point forward. This again poses several problems: she upstages the main villains one way or another, whether by joining them or doing her own thing. That, of course, pisses off fans who may be looking forward to seeing Cinder and Roman dealing with Godzilla. Not to mention, there's the question of how Ghidorah fits back into this: if too much of the story relies on the Godzilla characters, there's no reason to set this in Remnant. A potential compromise might be to start things a little further in the past: Emi wakes up first, gets out of there, and on Ghidorah's behest ends up becoming Cinder. This has the fewest problems, and is the solution I may ultimately go with, but it is still imperfect. Doing this means I basically have to write a second prologue, and that means the story takes even longer to get moving because the story of Emi becoming Cinder is basically irrelevant to the rest of the plot. Again, there are potential solutions to that, each with their own potential problems, but listing those out would spoil things should I decide to go this route.
The big lesson you should take away is this: try not to write yourself into a corner. And if you do, pause and think about it before you continue forward, as any potential solutions may not be as clear-cut as you prefer.