Using the Ultra Wormhole technology, Team Rainbow Rocket invaded the Festival Plaza, then the Aether Paradise to use its resources for their plans of universal domination. The player sees this happen on the news and is brought by Lillie to put a stop to them. Faba blocks them, hoping that allying with T.R.R. will get him a better position; however, the player takes him out and heads into the former mansion, which has been turned into T.R.R.'s castle. The Grunts attempt to stop the player, but Guzma holds them off. The player searches for a way to reach Giovanni, but runs into the villainous leaders of (Omega) Ruby's Team Magma, (Alpha) Sapphire's Team Aqua, Diamond/Pearl/Platinum's Team Galactic and X/Y's Team Flare: Maxie, Archie, Cyrus and Lysandre. With the exception of Cyrus, who wanted to go to his new world without spirit, the other three leaders planned on making them deranged plans come true in this new world; however, the player stops them all.
At that point, with all their defeats, they vanish, thanks to Colress using the Ultra Wormhole energy to send them back to the worlds they came from. Upon trying to reach Giovanni again, the player is stopped by Ghetsis of Team Plasma, who believes Giovanni would be a easier pawn to manipulate over N (as unlike his son, Giovanni is consumed by evil and is easy to trick using his ego). However, Ghetsis is also dispatched by Colress and the player enters Giovanni's room. After his defeat, Giovanni relinquishes control and flees. Faba is demoted and Giovanni begins planning a new scheme.
Team Rainbow Rocket is led by Giovanni, leader of Team Rocket. With his new Team Rainbow Rocket Grunts, he traveled through different worlds gathering all of the leaders of evil organizations from worlds where they succeeded in their goals, including:
- Maxie, leader of Team Magma, from a world where he used the power of Groudon to increase the land mass of the planet.
- Archie, leader of Team Aqua, from a world where he used the power of Kyogre to increase the sea level of the planet.
- Cyrus, leader of Team Galactic, from a world that he recreated without emotion using the power of the Lake Guardians & Creation Trio .
- Ghetsis, leader of Team Plasma and Seven Sages, from a world where he deceived the population into releasing their Pokemon, then conquered it using the power of the Tao Trio.
- Lysandre, leader of Team Flare, from a world where he used AZ's ultimate weapon, powered by Aura Trio, to wipe out most of all life to keep the planet beautiful.
- Counting Faba among "past villains" on the team, there's exactly seven "leaders" representing seven teams. This matches the number of colors in the rainbow like in the team's name.
- With the introduction of Team Rainbow Rocket, it's been officially confirmed the Pokémon reality has a multiverse. Counting the pairs of games as two separate universes and not counting any anime or manga, there's at least twenty of them.
- The current "main universe", where Let's Go, Pikachu!/Let's Go, Eevee!, HeartGold/SoulSilver, Omega Ruby/Alpha Sapphire, Platinum, Black/White, Black 2/White 2, X/Y and Ultra Sun/Ultra Moon take place.
- The alternate Generation I Era: Red, Blue, Green, Yellow, FireRed, and LeafGreen.
- The alternate Generation II Era: Gold, Silver and Crystal.
- The alternate Generation III Era: Ruby, Sapphire and Emerald. These universes are the ones mentioned by Zinnia where Mega Evolution is unknown, the Kalos war never happened, and the ultimate weapon was never even built.
- The alternate Generation IV Era: Diamond and Pearl.
- The alternate Generation VII Era: Sun and Moon.
- A world with expanded landmass where Team Magma succeeded.
- A world with expanded oceans where Team Aqua succeeded.
- A world destroyed and replaced by one without spirit by Team Galactic.
- A world where Team Plasma succeeded resulting in only Ghetsis having Pokémon.
- A world where only Team Flare is alive.
- Until Lysandre is reached, and if Cyrus is chosen before him, the leaders appear in the order of their games.
- Team Skull is the only criminal gang which isn’t part of the allied Team Rainbow Rocket, as the former gang had been reformed since the latter villainous team made its presence.