Sky Fortress/Sky Garden

After beating the legendary birds and obtaining the three orbs, the player will have access to the Sky Garden. In here, the player will face off with Rayquaza and see the conclusion of the bird trio's storyline.

Low Floors
Greenery decorates the walls, and the floor is grassy - water can be found relatively abundantly here. Stone tiles are embedded into the walls as well, and these stay present throughout the length of the dungeon.

Middle Floors
Hidden Highland-esque tiles start being used, and the water turns to pockets of air.

Upper Floors
Dark pines make up the walls in this section, with grassy flooring beneath the player.

Pokémon
''Pokémon in bold are recruitable. Please visit the Recruitable Pokémon page for more information.''

Upper Floors

 * Tropius
 * Tangrowth
 * Cradily
 * Liligant
 * Leavanny
 * Venusaur
 * Sceptile
 * Skarmory
 * Whimsicott
 * Vileplume
 * Parasect
 * Hoppip
 * Braviary
 * Skiploom
 * Carnivine
 * Grovyle
 * Leafeon
 * Fearow
 * Nuzleaf
 * Staraptor

Boss
On the Sky Fortress Garden's final floor, Sky Garden Rooftop, Rayquaza will appear and announce that he is free. He then calls over Slowking - the one the player meets earlier in the story - and turns it into a Ditto, revealing that the Ditto was the Slowking's original form, and that Moltres and Articuno were right; the Slowing/Ditto was not an ally to the player. The Ditto runs, and Rayquaza explains that he wanted to make the legendary birds weak so that he could escape and makes an offer to the player. The player rejects the offer and Rayquaza challenges the player. After defeat, Rayquaza vows revenge and leaves.
 * Rayquaza

Mystery Eggs

 * Seedot (Very Rare)
 * Cottonee
 * Oddish
 * Carnivine
 * Sewaddle
 * Hoppip
 * Paras
 * Petilil (F 50+)

Secret Room
In Sky Garden, Secret Rooms contain 4 Deluxe Boxes.

Items:
Relic Statue

Max Revive

Big Nugget

TM Swords Dance

Grass Dust

Dungeon Objective
The objective of this dungeon is to get experience, and get the Miracle Chest from the end box. Also, Rayquaza has a small chance to drop his Heart Slate for players to fuse with Mystery Part in order to be able to summon him in the dungeons.

Restrictions

 * Must have a flying-type on the team.

Tips

 * This dungeon contained a event Flying Pikachu for the first month of its release.
 * Rayquaza can be easily beaten if Imprison is used on it until all its moves are disabled.

Trivia

 * The bosses of Sky Fortress, along with the Mysterious Jungle boss, were given increases in stats.
 * Prior to the revamp, Sky Fortress had 70 floors.