Porygon2 first appeared as a Porygon in A Tale of Ninetales, when Blue bought it from the Rocket Game Corner. After Blue let Porygon out of its Poké Ball, it ran away, causing Blue to run into Red. Because of this, the two accidentally trade their Pokémon. During the three days that Red has Blue's team, he attempts to get them to relax and open up to him, with little success. They later traded back, while keeping the caring attitude that Red instilled in them.
In Striking Golduck, Porygon was Blue's last resort to fight Agatha's Gengar. Because Gengar would hide in the shadows and attack with Counter, Blue decided to use Porygon's Conversion to turn into a Ghost-type. Porygon was then able to counter Gengar's Counter attack but was unable to get Gengar out of the shadows long enough to land a finishing attack. Blue eventually managed to lure Gengar out of the shadows and had Porygon finish it with Psybeam.
In Once More into the Unown, Porygon2 uses its ability to move through cyberspace to enter into the Trainer Tower's computer system, "R". Using the Salac Berry that Blue gave it, Porygon2 quickly reaches the central nervous system and attacks with Zap Cannon, disabling it. Not long after this, "R" recovers and traps Porygon2 with a virtual lock.
As a Porygon, it was originally disobedient and would run away. However, after Blue and Red's temporary trade, it became more affectionate towards Blue and followed his orders from then on. As it is a man-made Pokémon designed to move around cyberspace, Porygon2 has been in use mainly via Blue's Pokédex as a surprise attack.