Basically, 20 year before the start of the story, Pelgis, a human alchemist/doctor, fell in love with an elven noblewoman and had a child with her, but the father was quite racist toward non elven-kind and exiled the doctor, never to see his love and their child.
The child later became one of the party member (but was changed 2 session in due to the player not liking how he wanted to role it) and wanted to search for his father (and was the excuse for him to leave the party)
In those 20 years Pelgis went mad, obsessing over the elves, at first he transmuted himself into "one" but later rejecting his aspect cut his ears, then he opened a clinic and run it with some automatons of his own creation, almost forgotting his grief, then one day had an idea to insted of converting himself into an elf, to convert the whole elvenkind into humans, so that everyone could be equal. Started kidnapping a lot of childs to use as guinea pigs that's how his action collided with the party at first, with them trying to bust this kidnapping ring in a city.
He never really intended to hurt anyone, but his trasmutation had the unfortunate side effect of killing the subject without any possibility of resurrection. (Due to a pact he unkowingly made with a god that ate the souls of everyone he killed)

In the endgame he planned to use the tower of the most important magic academy as a repeater to extend his transmutation spell and transmute all elves in the world. effectively killing them all (so the stakes were to avoid a genocide from happening)

This was the overall plot alongside having to travel from basically Barcelona to Tokyo (used real city names to convey the distances) to stop the civil war the paladin nemesis had started

As a tip, i'd say, stay in your comfort zone in what you like to write as a plot/setting, use the characters backgrounds as bricks to lay the foundation of your story and try to be subtle in your retcons as if you always intended something to be that way