The story takes place in a near-future alternate universe of the Pokemon world, in which Unova Pokemon are being migrated to Johto and Kanto as part of a government-backed experiment.
Olivia is a fourteen-year-old girl who is starting a journey in Johto after several years of special tutoring, hence why she is starting late. She hopes to use her quest as a way to find her father, who she is unaware passed away in a disaster five years prior. Her chaperone, Matt, was the one who tutored her on her late father's request; he has a goal of his own, which is to find Reshiram and use its flames of truth to learn more about his own relationship to what happened five years ago. They have also picked up two allies: Bunny, Matt's friend and colleague as an archeologist, and Nekou, a loud, sarcastic alcoholic with violent tendencies and a murky background.
However, strange things have begun happening to them. When Olivia went to Professor Elm's laboratory intending to get a Totodile as her official starter, he was missing and Professor Juniper happened to be there in his place, leading to Olivia being placed with an Oshawott she isn't totally thrilled with.
Meanwhile, Polaris, a mysterious Illuminati-like group, is planning something of biblical proportions on the continent. Team Rocket, their strength hobbled severely following their conflicts with Team Plasma - a wing of Polaris - in Unova, are jockeying into position to stop whatever Polaris is planning. To that end, the Team Rocket trio and Pierce
have been sent under the command of Ariana and Dr. Zager
to capture a piece of Meteonite, an element that fell on a meteorite, which will give them a leg up on Polaris's plans.
Right before the group arrived in Violet City, they encountered Nikolai, a young man with the ability to speak to Pokemon. However, he is actually N, but does not remember his true identity. During an encounter with one of the Shadow Triad, he was attacked with a poison, forcing Matt and the others to rush him to Violet City's Pokemon Center for stabilization.