>>55501466I would assume that each of those 5 segments (rouge, magenta, vert, bleu and jaune) are separate areas with their own boss(es) which take place in each respective plaza.
The idea is that the city has become overrun with Pokémon for some unknown reason. You're part of a research team who have to catch them in order to learn about what kind of environment they like. As you progress through each area, your Pokédex is used to assist the architect and each given area becomes "rebuilt" to accommodate the Pokémon with new parks, ponds etc.
You start in the Bleu Plaza (south west) which has early-XY mons like Flabébé, Fetchling, Litleo, then moving clockwise as you would through a playthrough of XY.
