The episode is infamous for certain repetitive visual effects which induced photosensitive epileptic seizures in a substantial number of Japanese viewers, an incident referred to as the "Pokémon Shock" (ポケモンショック Pokemon Shokku) by the Japanese press. 685 viewers were taken to hospitals; 2 people remained hospitalized for more than two weeks. Due to this, the episode has not been rebroadcast worldwide. After the incident, the Pokémon anime went into a four-month hiatus, and it returned on TV Tokyo in April 16, 1998, thus making the episode perhaps the most controversial episode of the entire Pokémon series. Since then, the episode has been parodied and referenced in cultural media, including The Simpsons and South Park.
Ash, Misty, Brock and Pikachu discover that the system used to transfer Pokémon from one Pokémon Center to the other is malfunctioning. On Nurse Joy's request, they go to Professor Akihabara, the one who created the Poké Ball transfer system. He tells them that Team Rocket stole his prototype Porygon, a digital Pokémon that can exist in cyberspace, and is using it to steal trainers' Pokémon from inside the computer system.
Akihabara sends Ash, Misty, Brock, Pikachu and his second Porygon into the system to stop Team Rocket, whom they learn have set up a blockade that stops Pokéballs from traveling the network. Porygon is able to defeat Team Rocket's Porygon, but Nurse Joy, monitoring the situation and unaware that Ash and the others are inside, has sent an anti-virus program into the system to combat what she thinks is a computer virus. Pikachu uses a Thunderbolt attack on the program, which manifests as "vaccine missiles", which causes an explosion. The group and Team Rocket successfully escape the computer, and with Team Rocket's blockade removed, the system returns to normal.
Twenty minutes into the episode, there is a scene in which Pikachu stops "vaccine" missiles with its Thunderbolt attack, resulting in a huge explosion that flashes red and blue lights. Although there were similar parts in the episode with red and blue flashes, two anime techniques, "paka paka" and "flash" made this scene extremely intense. These flashes were bright strobe lights, with blinks at a rate of about 12 Hz for approximately six seconds.
At this point, viewers started to complain of blurred vision, headaches, dizziness and nausea. Some experienced seizures, blindness, convulsions and loss of consciousness. Japan's Fire Defense Agency reported that a total of 685 viewers – 310 boys and 375 girls – were taken to hospitals by ambulances. Although many victims recovered during the ambulance trip, more than 150 of them were admitted to hospitals. Two people remained hospitalized for more than two weeks. Some other people had seizures when parts of the scene were rebroadcast during news reports on the seizures. Only a small fraction of the 685 children treated were diagnosed with photosensitive epilepsy. This phenomenon was later called "Pokémon Shock".
Later studies showed that 5–10% of the viewers had mild symptoms that did not need hospital treatment. Twelve thousand children who did not get sent to hospital by ambulance reported mild symptoms of illness; however, their symptoms more closely resembled mass hysteria than a grand mal seizure. A study following 103 patients over three years after the event found that most of them had no further seizures. Scientists believe that the flashing lights triggered photosensitive seizures in which visual stimuli such as flashing lights can cause altered consciousness. Although approximately 1 in 4,000 people are susceptible to these types of seizures, the number of people affected by this Pokémon episode was unprecedented.
An article in USA Today reassured parents that "American children aren't likely to suffer seizures provoked by TV cartoons", because U.S. networks "don't air the graphic Japanese cartoons known as 'anime'" with their "fast-paced style of animation", although anime has become more prevalent on American television since then. The incident, which was referred to as the "Pokémon Shock" (ポケモンショック Pokemon Shokku) by the Japanese press, was included in the 2004 edition and the 2008 Gamer's Edition of the Guinness World Records book, with the honor of holding the record for "Most Photosensitive Epileptic Seizures Caused by a Television Show".