After a brief search for BlacephalonUS/StakatakaUM, the player takes a break at their house. Sophocles suddenly comes in, saying someone took over the Festival Plaza, and both he and the player immediately teleport there.
Upon arriving, the player discovers the castle is now sporting a more sinister design adorned with screens, each displaying a letter "R" on a rainbow-colored background. Sophocles explains someone must have hacked Festival Plaza, and both he and the player rush into the castle only to see a group of Team Rainbow Rocket Grunts, one of them proclaiming the castle now belongs to them. Sophocles digs into the Festival Plaza's configuration and realizes it has been patched so that nobody can use their Pokémon while inside. While Sophocles wonders how they will deal with the intruders, one of the Grunts inadvertently tips off the player they could battle them using other people's Pokémon in the Battle Agency, which Sophocles manages to activate despite his admin account having been downgraded by the hackers. While the player battles a Team Rainbow Rocket Grunt in the Battle Agency, Sophocles manages to hack into the Festival Plaza's programming and restore his admin privileges. Upon coming back, the Grunts surround both Sophocles and the player, one of them even attempting to physically assault the player, but Sophocles manages to ban them from the Plaza, teleporting them out instantly. The castle keeps its new design, however.
Upon their return to the real world, Sophocles thanks the player and leaves. The player's mother then shows her Meowth's new trick: it learned how to turn on the TV by observing her. That's when the player watches an interview of Lusamine at Aether Paradise.
On TV, Lusamine elaborates on the recent events on Poni Island involving Necrozma and assures everyone the incident is dealt with. During the interview, Wicke and Faba stand behind her and the latter quietly slips away. Suddenly, an Ultra Wormhole appears in the sky and the cameraman gets pushed by a Team Rainbow Rocket Grunt and drops his camera. A mysterious figure arrives and says the studies and technologies that are being worked on at Aether Paradise will be of great use to Team Rainbow Rocket.
Lillie comes in and asks the player to join her back at Aether Paradise, alarmed and confused by the news report. After getting there, they meet up with Wicke, who tells them Team Rainbow Rocket took over Aether Paradise for reasons unknown and took Lusamine hostage, she also recalls she once heard of a similarly named Team Rocket during her travels in Kanto. The player and Lillie run into a group of Grunts on their way to the mansion, and Lillie is revealed to have become a Pokémon Trainer herself, now in possession of a Clefairy. After dealing with the Grunts, they discover that Lusamine's mansion is no more, and in its place stands its warped version, the Team Rocket's Castle. That's when they are welcomed by Faba, who reveals he sold out Aether Paradise to Team Rainbow Rocket in order to further his career, infuriating Lillie. A battle ensues, and Faba eventually gives up and lets the duo make their way into the castle. Lillie walks into Lusamine's room, now colored in red, and realizes they need to use the teleporter hidden inside, but the door leading to it is locked. On their way out of the room, two more Grunts challenge them to a battle, but another ally suddenly shows up and helps defeat the Grunts: none other than Guzma.
The Grunts retreat, opening two doors in the process. Lillie stays behind while the player explores the first floor of the castle, encountering more Grunts, and ultimately running into Maxie and Archie, who occupy offices on the opposite sides of the castle. Both reveal they came from alternate worlds where they have achieved their goals of, respectively, using Groudon to expand the landmass and using Kyogre to expand the sea, and have been transported to this world right after having done so. The player battles them, opening the doors to the second floor of the castle in the process, and returns to the hallway, where they see Guzma easily holding back two Grunts. The Grunts reveal that in order to open the door and activate the teleporter in Lusamine's room, the player must proceed to the second floor. Just at this moment, Maxie and Archie arrive and are surprised to see each other. Even after they realize they came from different worlds, they start arguing, only to suddenly vanish into thin air.
The player explores the second floor, where more Grunts hold guard and two more villainous team leaders hide.
The player meets Cyrus, who asks them if this world he found himself in is the world without spirit he always wanted. The player and Rotom prove him otherwise. After a battle, Cyrus admits defeat and helps the player out, admitting he only wants to get back to the world without spirit he managed to create.
The player meets Lysandre, who tells them of the ultimate weapon he managed to create and use in his world, and shows two buttons on the wall, one of them activating the ultimate weapon in this world. He offers the player a chance to save the world or doom it by pressing one of the buttons, but no matter which one the player presses, the ultimate weapon starts charging up, and will only turn off if the other one is pressed. Lysandre fights the player to prevent them from doing so, and is defeated.
After the player swipes a key card in Cyrus's office and presses both buttons in Lysandre's office, the door in Lusamine's room opens and the teleporter activates. When the player and Lillie get ready to use it, Ghetsis suddenly comes out of it. He tells them he has been summoned to this world to separate people from Pokémon, and is planning to use Team Rainbow Rocket's boss to achieve his goals. A battle ensues and Ghetsis loses. He breaks down, strikes down Lillie and threatens to kill her unless the player gives up on all of their Pokémon on the spot.
As the player hesitates to comply, Colress suddenly reveals himself, having used his inventions to follow the player while remaining invisible and send other villainous leaders back to their worlds. Even though he acknowledges this Ghetsis is not from his world, Colress berates him and teleports him away. He explains to the player and Lillie that what happened to Lusamine's manor is a product of multiple dimensions converging, and he can restore it, but only after the player defeats the leader of the villainous team.
Lillie and the player take the teleporter and are welcomed by the mastermind behind the invasion, Giovanni. Lillie also discovers Lusamine unconscious and, according to Giovanni, brainwashed with an Ultra Beast's toxins. The player fights and defeats Giovanni, who gracefully retreats, but not before promising the player they will meet again. Suddenly, the player and Lillie find themselves in Lusamine's trophy room, the manor having been reverted to its normal appearance. Lusamine wakes up, shaky, but still herself, and Guzma and Colress join them. Amidst the celebration of their victory against Team Rainbow Rocket, Faba suddenly walks from behind one of Lusamine's trophies. He tries sucking up to Lusamine, but gives himself away as a traitor almost immediately and hastily leaves.
The day is saved and Faba has been demoted to an intern. Watching as life at Aether Paradise returns to normal, Giovanni wonders out loud what other worlds he could unleash his schemes upon and teleports away on his own.