My guess for how this works is that sometime around the seventh gym (the area the main event normally occurs) Team Flare is using Az's ultimate weapon and destroying the ecosystem. The only thing that can stop it is Zygarde. You go on quest to find it, only to discover it is stuck in its core form, unable to find other cells to join up with. You catch it, and it is then up to you to travel across the region, powering it up until you reach 50%. You try and fail to stop Team Flare, so you must continue your search until you find all of the cells, and create Complete Zygarde, which does have the power to stop Team Flare. Probably after this event, you can take away and give Zygarde cells as you wish.
The idea actually sounds pretty cool. I just wish that one of the forms wasn't a dog.