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It actually wouldnt even be that hard to give Zygarde a good role in the game just expanding on what we have now
You meet Dexio and Sina and start the quest to collect the cores as usual, only this time for every 10 cells you find, they'll call you up and drop some deepestlore on you, such as why he's in the region or what his relation to other legendaries are
When the climax of the story goes down, you see a cut scene of cells flying out of your bag and from all over the region, combining to fullfil his duty
Later you collect 99 cells/cores all over the place but the last one in Resolution Cave is locked until you get all the others, at which point they all combine and you actually get to battle him in his perfect form to prove your worth
