An old woman is standing outside the ruins of the collapsed Silph Co. building. Shifting through the remains with her staff, she smiles to herself as she finds the Pokémon Badge Energy Amplifier.
Two years after the Pokémon League and all is well in Pallet Town. A mailman riding a Ponyta is surprised when his mount bolts uncontrollably, nearly getting into an accident when a local intervenes, releasing his Venusaur to calm Ponyta down. Looking through the mail, the mailman explains that he has a letter for Red, and asks if the young man knows where Red is, to which the boy reveals himself to be none other than Red, the winner of the ninth Pokémon League Championships. Leaving the mailman stunned, Red opens up his mail to find a note of a challenge. Elsewhere, in northwest Kanto, Bruno of the Elite Four performs his rigorous training, just as Lorelei informs him that Lance had a letter sent to Red in his name, as a part of Lance's plans.
One month later at Professor Oak's Laboratory, Professor Oak and Misty are having a video chat. The professor points out that Red has been absent since he received the letter and the flood of challenges he received after his victory at the Pokémon League. Oak notes with dismay that as a result, Red had neglected his duty of completing the Pokédex, which the professor needs urgently to help document the new Pokémon beyond the previously known 151 species. Misty voices her irritation at Red's neglect, remarking that the boy had even asked her for advice on becoming a Gym Leader, as Oak muses how Blue and Green, the other Pokédex holders of Pallet Town, have likewise left on their own journeys.
Just as Oak tries to read the letter that Red received to Misty, which proves to be difficult given its intelligibility, the two are alerted by sparks coming from the laboratory's front door's doorknob. Expecting Red's Pika, the Professor opens the door with insulated gloves, but to his and Misty's surprise, Pika is not only alone, but severely injured as well.
Agatha searches the ruins of Silph Co. and finds the Pokémon Badge Energy Amplifier.