Team Rocket's Castle's entrance room and bedroom have identical layouts to the ones seen in Lusamine's mansion. When first entering the bedroom, Lillie will try to activate the warp tile to the center of the castle, but is unable to even open the mirror door leading to the tile. Upon exiting the bedroom, two Team Rainbow Rocket Grunts appear to stop the player and Lillie. However, Guzma also shows up and helps the player in defeating the two Grunts in a Multi Battle. After being defeated, the Grunts flee, opening the gates to the southern wings of the castle in the process. Lillie will then station herself in the bedroom, healing the player's Pokémon whenever she's talked to, while Guzma will stay in the entrance room.
At the end of each of the castle's four wings lies a room guarded by a pair of Team Rainbow Rocket Grunts, who battle the player consecutively before letting them through. Inside each of these rooms is a villainous team leader from an alternate reality, in which they succeeded in their plans due to the lack of a player character to stop them. Each of them also wields a Legendary Pokémon from their native region. Once the player defeats a leader in battle, they will provide the player with a method to advance further into the castle, simultaneously activating a one-way warp tile back to the entrance room.
Several item balls found here are actually Electrode, which will attack the player if interacted with. If they are not defeated or caught, they will remain on the floor.
In the southwest wing, the player must navigate through a maze of warp tiles in order to reach the end. Some of these paths lead to a dead end. In one room, different rows of warp panels are separated by walls of Team Rainbow Rocket Grunts standing in rows across the room. The end of the wing has a room occupied by Team Aqua leader Archie. After he is defeated, he will allow the player to press a secret switch behind a painting.
In the southeast wing, the player must solve three memory puzzles in order to advance through the three puzzle rooms. The player must first press the button in the middle of the room, causing the four colored panels on the floor to light up in a certain order. The player must then step on the tiles in the given order. If they step on a wrong tile, the puzzle will be reset. Each room has three possible puzzles to be generated. If the player presses the button again before stepping on any of the tiles, a new puzzle will be generated. The first puzzle requires memorizing the order of four panels, the second one requires six, and the third one requires eight. In the second puzzle room, a Team Rainbow Rocket Grunt will strike a pose in an attempt to distract the player in the middle of them trying to solve the puzzle, while in the third room, the player's attempt to solve the puzzle will be distrupted by a pair of Team Rainbow Rocket Grunts, who in turn challenge the player to a battle while they're solving the puzzle. If the third puzzle is reset after a Grunt has been defeated, said Grunt will not battle the player again. Once a puzzle is solved, a warp tile leading to the next room will be activated. At the end of the wing is a room housing Maxie, the leader of Team Magma. Like Archie, Maxie will allow the player to press a secret switch behind a painting after being defeated.
After the player has pressed both secret switches, the gates to the northern wings of the castle will open in the entrance room. Two Team Rainbow Rocket Grunts will emerge from the gates when they're opened and try to attack Guzma, only to be physically held back by him until all the evil team leaders have been defeated. Archie and Maxie will also appear in the entrance room, and, upon noticing each other, challenge each other to a battle to see which one of them gets to rule Alola. However, before they can even exit the building, they are warped away by an invisible force.
In the northwest wing, the rooms are filled with spin tiles, similar to the original Team Rocket Hideout in Kanto. This wing's final room is occupied by Team Galactic leader Cyrus. Once he's defeated, he will hand the player the Galactic Key, which they can use to activate a machine on the wall and remove one of the two last obstacles.
In the northeast wing, the rooms are guarded by Meowth statues. If the player steps into a statue's line of sight, they will be warped back to the beginning of the room. By interacting with a Meowth statue from behind, the player can push a button to turn the statue into a direction marked by an arrow on the floor, allowing them to advance through the room unnoticed. If the player is warped back to the entrance, any rotated statues will be reset. The statues will also be reset when the player leaves the room. The room at the end of the wing houses Lysandre, the leader of Team Flare, who forces the player to make a choice between pressing one of two buttons, with the wrong choice leading to him activating the ultimate weapon. No matter which button the player chooses, the ultimate weapon will be activated, but once he's defeated, Lysandre will allow the player to press the other button as well, deactivating the weapon and removing one of the two last obstacles blocking access to the center of the castle.
Once the player has beaten both Cyrus and Lysandre, the mirror door in the bedroom will have opened and the warp tile behind it has become active. However, once the player tries to step onto the warp tile, Team Plasma leader Ghetsis will appear through it, explaining to the player and Lillie that he's planning to make the leader of Team Rainbow Rocket his "king" to rule above all existence, similar to how he had previously made N the king of Team Plasma to rule Unova, and challenges the player to a battle to keep them from foiling his plans. Upon being defeated, Ghetsis flies into a fit of rage and starts threatening Lillie's life. However, she's saved by the arrival of Colress, who then proceeds to warp Ghetsis back to his own reality, allowing the player to move forward.
In the Trophy Room at the center of the castle, the player will encounter Giovanni, the leader of Team Rainbow Rocket, who tells the player about his plan to conquer all realities with an army of Ultra Beasts. He's also taken Lusamine hostage, planning to turn her into his loyal servant. To keep the player from interfering with his plans, Giovanni then challenges them to a battle. Once Giovanni is defeated, he declares that although he will step aside this time, Team Rainbow Rocket will never fall. As he warps away, the castle is restored back to its state as Lusamine's mansion by one of Colress's inventions.