The anti-virus program mistook Ash and friends, who were riding Porygon, for virus and fired a missile on them. Pikachu Thunderbolted the missiles, which caused the entire screen flash red and blue. I think a bit similar visual effect appears in certain other anime as well, for instance Sailor Moon, but in Electric Soldier Porygon it lasted much longer and that's why hundreds of Japanese kids had epileptic seizures. As a result, Pokemon anime was banned for a while even in Japan, and Holiday Hi-Jynx and Snow Way Out! were shown in a weird place as they were originally meant to be shown in Christmas time. Notable differences were there was no Togepi in those episodes and Ash's Charmander was still Charmander.