Stopping in yet another Pokémon Center, Ash, Misty, and Brock find a very distressed Nurse Joy. It seems that something is wrong with the network links between the Pokémon Centers, and she is finding it difficult to send and receive Pokémon from her cousin in Viridian City. To fix the problem, Professor Akihabara is investigating. He soon discovers something, and rushes from the room, back to his house. Ash, Misty, and Brock are as curious as they always are, and ask Joy for directions to him. When they arrive, they are greeted by the giant head of Akihabara, which Brock quickly identifies as a hologram. This takes them to a large tube inside a laboratory, and the real Akihabara begins to talk to them. He explains that some Pokémon thieves had broken into his lab, to steal a prototype Pokémon he had been working on. In an attempt to stop them, he transported them into the "computer world". Unfortunately, once inside, they set up blockades to stop Pokéballs being transported between Pokémon Centres. Without their consent, the Professor transports the trio into the computer world also, with a new version of Porygon, to stop Team Rocket. Once inside this new world, the Porygon grows, and Ash, Misty, Brock, and Pikachu ride on it's back.
They soon find Team Rocket, and a battle begins. Team Rocket send out Arbok and Weezing, who are quickly defeated by Porygon, which has used a conversion attack, giving it a "Weezing skin". From underneath the losing Pokémon, Jessie releases her prototype Porygon, complete with a little Team Rocket flag on its tail. This battle lasts considerably longer, each Porygon changing it's shape to counter the others attack. The Professor appears next to the twerp trio on a little screen, and tells them to remove the barriers, so the Pokéballs can flow again. They obey, and begin to remove them. Jessie, James, and Meowth see this, and run towards the Ash, Misty, and Brock, but are caught in the stream of Pokéballs rushing past. Pikachu takes advantage of this, and without even the order from Ash shocks them. Their Porygon is then pushed right into them, and they are sent "logging off again", along with the Porygon. As Ash, Misty, and Brock wave goodbye happily, the Professor notices something, and disappears. It seems the Pokémon Center is accessing and loading some software in the computer world. What could they be doing? Akihabara calls Joy on the video phone, and she tells him that there is nothing to worry about, everything is under control. She has hired someone to install anti-virus software to destroy the files that shouldn't be there, and that means Ash, Misty, and Brock!
The anti-virus software rushes to the scene in the shape of a futuristic looking ambulance, Ash and friends still removing the barriers; the Pokéballs still aren't moving as they should. He spots a "Stop" sign Team Rocket have put up, and is about to destroy it when the Professor screen returns, to quickly warn them about the approaching vaccine. Misty and Ash don't seem to care, so Brock explains that it will find them and "delete" them. Misty and Ash go into a state of panic, just as the anti-virus software arrives. Spotting Ash and co.'s, and targeting Misty, its sides fold down revealing vaccine missiles. Ash calls down Porygon, and they get on its back. They spot Jessie and James running in the opposite direction, towards the vaccine, Meowth on their Porygon flying beside them. Jessie and James also see them , and shout at them, thinking they are too afraid to battle again. Ash tells them that they should be running as well. The ant-virus software then launches two missiles, destroying TR's "Stop" sign. All the Pokéballs then fly towards Team Rocket, and they are pushed along with them. The anti-virus is following, and prepares to launch more missiles at them. Meowth then flies down to them on the Porygon, Jessie gets on, and James is left hanging on it as it soars higher. The anti-virus then targets them again, and spins around, changing into a large syringe. It too flies up behind the two Porygon. This time it fires four missiles, one hitting TR's Porygon, knocking it down, the next following it. Ash And Co.' Porygon is able to dodge the next, but is hit by the other. One more stuns the Porygon, and Ash and co.'s fall off. Shaking off this shock, the Porygon dives, and is able to catch them in time. The Professor screen sees a portal, which he tells them will let them exit the computer world. Team Rocket fly behind them, desperate to escape too. The guy who installed the software is controlling it's activities, and still detecting invading files, he takes drastic measures. The front of the syringe splits open, revealing a large gun. It fires a huge sphere of light at TR's Porygon, engulfing them. With the huge explosion, there is a system error, and the guy loses control of the anti-virus, and it begins to fall. Team Rocket wake up inside a small box, and as James demonstrates, sliding down the wall, they can't get out. Meowth explains that it would be easy to get out if they still had Porygon. Jessie asks where it is, and Meowth points. They Porygon is laying unconscious on the floor. Jessie picks it up, and it's head droops back. Ash and co.'s are about to escape through the portal, but Ash and Misty want to save Team Rocket. The guy has control of the anti-virus again, and it takes aim at the trapped Team Rocket. It fires, but two vines get to Jessie, James, and Meowth first, and they are lifted to safety by Bulbasaur.
Porygon is finding it hard to cope with the increased wait, and the vaccine software takes aim again. It fires four missiles, and the Porygon just can't get away. Pikachu shocks two of them, and they explode before they hit. But, there are still two more! Luckily, the Porygon goes through the portal just before they hit. However, so do the missiles, and a large explosion follows, destroying Professor Akihabara's home! Surprisingly, Team Rocket say "Thank you" before running way. The Professor looks at his destroyed lab, and falls to his knees, picking up some machinery. He can no longer enter the computer world! Ash jokes that it looks like his "system has really crashed this time". Ash, Misty, and Brock return to the Pokémon Center, and everything is working fine, and our friends continue on their journey...