First, to make things clear: this challenge isn't about a strict crossover between Xenoblade Chronicles X and Gate: Jietai Kare no Chi nite, Kaku Tatakeri. The Gate part being the closest example of a fantasy world clashing with the modern one. The idea is to put a Xenoblade Chronicles X plot but in a fantasy world, or even another dimension, isekai style, but with different characters and situations. Through Ocean Star is also a good example. The White Whale will still be in Mira, so, apart from some mention, none of the canon characters will appear.

So, you can make all the OCs that you prefer, being soldiers, civilians, BLADE(yes, some coincidences may occur) members, kings, princesses, gods… everyone you want and of the races you prefer.

The main backstory or idea, is that one of the Arks of Project Exodus is destroyed in the planetary evacuation, and, somehow, appear intact at an unknown system or the orbit of some habitable planet and, being the best option, descend to it. Or you can use the wormhole excuse or "being in the same universe" one (the last one may guarantee a Ganglion attack and/or the possibility to contact Mira and New Los Angeles). The integrity of the ship in the end is optional and will affect the resources that the Earth refugees have access to. e.x.:the Lifehold.

The use of mimeosomes is optional, but you can't deny their tactical advantage if they have the Lifehold, to have pseudo-immortal troopes, or, in simpler terms, a resurrection system.

Like every Xenoblade, all Arts must make act of presence, including classes and Skells. The possibility of magic or other mystical or supernatural powers for the Earth natives is also optional. And viceversa with the fantasy world natives. I think a medieval knight piloting a futuristic giant mecha is something totally fit for Ocean Star.

The themes that must be present will be of some of the series mentioned previously, such as, pacifism, war, racism, god-like arrogance… There are fanfics, such as Fae is Foul or Halkeginia Online (both SAO/Familiar of Zero crossovers), that could give you inspiration, especially in politics. Being forced to escape their exploding homeworld from an intergalactic war that they were caught in, Earth's humanity will give it their all to be able to coexistence with the natives, but don't take them wrong, if they must defend themselves, they will (with firearms and giant robots), so tensions will be constant.

All in all, is a fantasy/isekai story with Xenoblade X elements and terms, Gate and Star Ocean political and philosophical issues and completely original. You can even discuss your OCs (Xenoblade X customization to Earth characters with liberty) and plot myself, but I ABSOLUTELY don't own them, I only give the idea and I am not an experienced Beta Reader or writer. If you want to contact me, PM me.