At the Sky Pillar, Wally continues his training with Norman. In battle, Wally faces Norman's Spinda and Norman's Slaking with his Kecleon and Flygon. By exploiting Slaking's Truant Ability, Wally quickly gains an advantage until Norman uses his Spinda's Skill Swap to switch its Ability with Slaking. With this tactic, Norman manages to defeat Wally easily. Although Wally is discouraged by the loss, Norman states that Wally fought well enough to force him to go all out.
Wally feels guilty for using the Pokédex, as it doesn't rightfully belong to him. As well as the Pokédex, the Treecko Wally used has evolved into Grovyle as well as Ruby's Rara evolving into a Kirlia. Norman attempts to erase Wally's guilt by stating that Grovyle most likely belongs to his friend, Professor Birch, and that since he gave Ruby Rara, he has no problem with Wally using it. Wally becomes distraught again and begins asking why Norman is doing this. When Norman asks why, Wally points out that he doesn't have the right to train Pokémon that don't belong to him.
Wally asks why they're still in the Sky Pillar when they could be helping the crisis plaguing Hoenn. Wally yells at Norman, demanding to know the real reason why he's training him. Norman decides to reveal the real reason, but the tower begins collapsing before he can start. As they dodge the rubble, Norman gets a call from Scott, who had snuck aboard the Pokémon Association headquarters.
With the information he gathered, Scott reveals that the other Gym Leaders had fought Team Aqua and Team Magma in order to stop Kyogre and Groudon, but failed. Scott goes on to say that after the leaders of the teams failed to control the Red and Blue Orbs, the Orbs went to new controllers, Professor Birch's daughter, Sapphire, and Norman's son, Ruby. As Scott leaves the headquarters, he tells Norman to hurry with the third Legendary Pokémon.
Although Wally doubts what Scott said, Norman reveals that Scott is a person who searches for talented Trainers and is to be trusted. Norman decides to take this time to reveal what he really trained Wally for and sends him to stand on a circle on the floor. Norman pulls a switch that causes a beam of light to pull Wally and his Kecleon upwards. When Kecleon begins writhing in pain, Norman tells Wally to put it back in its Poké Ball, as the beam repels Pokémon. After passing to the next area, Norman tells Wally that they will awaken the ancient Pokémon together.
As Wally moves through the passageways while Norman pulls the chains, Norman reveals that the area is designed so that only an adult and child will be able to pass through. Wally eventually makes it through, and finds himself standing before the Sky High Pokémon, Rayquaza. Due to Rayquaza hibernating, it is surrounded by a layer of poisonous ozone, which prevents Wally from getting near it. Remembering what Norman told him, Wally realizes that Norman had intended to do this mission with Ruby, and that he is only a substitute.
Wally quickly shrugs it off as he sends out Rara to use Imprison on Rayquaza. In his head, Wally feels glad to contribute to saving Hoenn in any way he can. Wally sends out Grovyle, which uses Bullet Seed to rip a hole in Rayquaza's ozone layer, awakening it. Rayquaza, now fully awakened, bursts through the top of the Sky Pillar, destroying the top of it. As Wally lies on his Flygon exhausted, he notes that Norman isn't there anymore, and must have gone to Sootopolis City with Rayquaza.