As far as the Web Novel goes, from what i remember reading notes about it (didn't feel like read the whole story so read only summaries), at the end of the story Leon dies, and so are a few of the other girls.
Marie is the only surviving one, and she ends up wishing that Leon gets a better next life while not remember anything about his current life.
Later it gets revealed that the Leon of Main Story is the same one as the one from the Marie Route except he doesn't have any memories about Marie Route, and only has memories of his life from Japan.
It is also confirmed that the Marie in Main Story is different from Marie in Marie Route, as she is from a parallel world, unlike the Main Story one who is same world as Leon.
So, basically this makes Marie Route as a prequel to the Main Story.