Okay, let me see if I've got this.
Zygarde attacks the town the MC is staying in to try and get to him, thinking he's going to cause an apocalypse, she flees from the Ship due to all the Legends on board but the MC gives chase through the town before she can cause too much damage, the other Legends are busy keeping the town safe so the MC is alone for the fight.
That does sound like an exciting plan if I can make it work!
Zygarde being similar to Rayquaza sounds like a good idea, they'd probably team up together and act like enforcers whenever the other girls get too rowdy, that's after she's been caught of course!
Her warning the MC about Eternatus makes sense too, definitely potential for a rivalry there!
I don't think I'll use the festival/orgy scene though, it's not that it's a bad plan, it's just not what I really want to write, if I did though I'd have to leave out the images, generating enough to show a scene like that would get pretty tiresome.