After a few years in training, Giovanni is ready to resurrect his infamous organization: Team Rocket. The group was able to recover after a crucial defeat in Goldenrod City when a trainer managed to thwart the plot using the Goldenrod Radio Tower to send out sound waves that made Pokemon weak, angry, or even evolve. Now with their leader back, Team Rocket is able to focus once again on stealing Pokemon and attempting to conquer the Kanto region.
Some stolen documents from the Pokemon G-Men found by the champion, Lance, suggest that Team Rocket is secretly using microchip technology and implanting these devices in Pokemon in order to brainwash them into blindly attacking anyone or anything, as well as cause all sorts of chaos. Such a device created by the G-Men has the ability to neutralize the effects, though Team Rocket knows of this and is searching for a way to render these devices useless, and this plan will not only help render the devices useless, but it'll also be able to help them conquer the region.
While most of their operations remain underground and hidden until they unleash one of their brainwashed Pokemon to cause chaos(and even do their own bidding) until a city surrenders and pays its respect to the group, Team Rocket occasionally goes around town attempting to steal Pokemon, as well as do other crimes like robbing a bank.
As a starting trainer, you have been caught up in all of this. While you expected to only be traveling the Kanto Region, getting your first Pokemon, catching Pokemon, and fighting in gym battles or contests, you will be employed by Lance himself to help stop Team Rocket when needed He'll also give your group one of the neutralizers in case you get attacked by one of their brainwashed Pokemon. Fortunately for you, Team Rocket isn't always out terrorizing the region so you still have a fair amount of time to catch Pokemon, bond, train them, fight in the gyms or contests, and just have fun while you can.
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