Bunch of hacker nerds, their evil plan is to hack the storage system to steal pokemon directly and hold them for ransom. Region's resident storage system expert comes up with a non-networked portable pc but can only hold a limited amount. Offers to hold on to extra pokemon for the player i guess, for those people who have to catch everything they see. Upgrades throughout the game would be storage capacity and increased functionality. For example gain the ability to heal your Pokemon, teach them new moves, ev train, etc. all from the convenience of your pocket.
Partway through the game a crazier member of the organization breaks away and forms his own group, they are straight up hacking pokemon. Their pokemon have unusual moves or abilities, and later on even typings or stat changes.
Original bad guys team up with you (they may be crooks but they still care about Pokemon) to take them on. Big bad loses it completely and transports his consciousness into a virtual reality. For the final showdown you are traversing a totally glitched out world, being attacked by hideous monstrosities (including a reference to Missingno, and that is the only gen1 pandering in the game.) After you beat the boss he regains some sanity, gives you a floppy disc with the code to undo everything and free everyone's pokemon, but stays behind in the decaying glitch world.
Kind of ripped off cyrus there but whatever. Either that or "oh i'm sorry" and then nobody cares about all the bad shit that happened anymore
