The Cult of Darkrai is the three-floored secret base of the Darkrai Cultists, where human sacrifices are made in order to summon the Legendary Pokémon, . The player begins their adventure here.
- After reading the dialogue between two cultists and their leader, Persephone, the player is saved from a 's by a .
- With Mew following behind, explore the remainder of this floor before heading up a set of stairs at the end of the path.
- Two paths exist on this floor, with only the path to the south being open at the moment. Begin to head down towards the stairs leading to the floor above.
- As the player is about to head up the stairs, read the dialogue that appears explaining Mew's ability.
- After heading up the stairs, go up towards a blood-stained altar with two statues of Darkrai on each side.
- Stand in between the Darkrai statues and interact with the dried blood to obtain the DNA of a Darkrai Cultist.
- Talk to Mew and transform into a Darkrai Cultist before heading back downstairs.
- Interacting with the door in front of the previously inaccessible path to the right allows the door to open. The player may head back down the stairs to the left to pick up a few previously unobtainable items.
- After passing the scanner-activated door, follow the path leading upwards until the player comes across another staircase leading to the floor above.
- On the next floor, head up to witness a scene involving the sacrifice of a Darkrai Cultist and Darkrai's refusal to obey Persephone.
- After Persephone announces that she will check on the player's condition, head back downstairs.
- Once downstairs, head back in the direction the player previously traversed, but this time ignore the path leading back to the scanner-activated door and follow the path leading downward.
- Exit the base through the doorway at the end of the path.
- B1F; in the cell located two doors down from where the player was kept
- B1F; in the locked cell located five doors down from where the player was kept
- 1F; on a table directly above the exit to Shade Forest
- 1F; on a table in the room full of acid pits
|- style="background: #FFFFFF;" | align="center" | | align="center" | Ice Heal | align="left" | 1F; on a table directly above the exit to Shade Forest
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|- style="background: #FFFFFF;" | align="center" | | align="center" | Master Ball | align="left" |
- 2F; when you first enter the base from Shade Forest, go to the northernmost part and go upstairs to the second floor. Use Seed Flare to purify the water in the area, then surf south to get to the Master Ball.