Although Giovanni funded the development of Porygon; it's source has hit the Internets.

After Team Rockets' fall/disbandment, Giovanni ordered the Source Code leaked online: He figured that everyone who isn't a retard can compile their own, and that would create a demand for the Porygon Updates/Upgrades. He built a company around selling this as a product to the Community.

Then a Hacker Group, many of them former Plasma Members, decided that if data of Porygon could be Compiled into a real pokemon: why not the data of all the other pokemon Trainers store on "the PC Network"?

Cloning this data, and letting these pokemon out: the group called "Team Cypher" seeks to do what Aqua could not: Overwhelm trainers with pokemon surpassing, if not equalling the Trainer's finest.