>>44175984Surprised this hasn't been used in both this thread and the actual games:
AI created to bring all services to a new level for efficiency. It turns on a red herring (meant to look like the evil team leader but is actually a good guy who's just as shocked as you with the betrayal) after feeling it wasn't being used to its full potential.
It will have a moment like the Gen 3,4,7, & 8 Legendaries where its rising up caused an impact on nearly everything you use such as your PC (Box Link would be down as an extension) and PokéCenters/Marts are down because they can't access the Internet to order any supplies. During that section of the story, you'll have to either be a refugee as you'll be on a hit list because muh chosen one or you'll have the creator of the AI follow you to support to stop it out of guilt (think the Stat Trainers from Gen 4 but hanging around longer).
As for the battle against the head AI, it'd use 5 of your own Pokémon from your PC (remember that it has access to everything including your Boxes). In case you don't capture anything besides your main party, the game would have mandatory side quests prior to this where you need to take down a rampaging Pokémon (think Totems). If that seems too complicated, give it obvious things like Metagross. The last Pokémon would be an alternate evolution of Porygon2 in which it came out perfectly and is an extension of the AI.