On top of Rayquaza's head, Ruby notices the figure hidden behind the layer of ozone is his father, Norman. As she lays dying, Courtney reveals that after her defeat at the Rusturf Tunnel she wanted to become Ruby's friend. Courtney reveals that in order to do this, she had to learn everything about Ruby, including that his father is the Gym Leader of the Petalburg Gym. Upon learning that Norman failed his Gym Leader inauguration test, she went to find out why he didn't retake the test in the five years since he initially failed it.
Courtney reveals that Norman didn't retake the test because he was banned from doing so for five years and was forced to look for Rayquaza, which he had lost. She states that the Pokémon Association Chairman intended to use Rayquaza to subdue Groudon and Kyogre. Ruby, learning that with Rayquaza and the Red and Blue Orbs he and Norman can stop Groudon and Kyogre, jumps on top of Rayquaza. Ruby, in his head, thanks Courtney for her help and considers them comrades from the start because of their love for Contests.
Ruby tries to talk to Norman, but when he is ignored, he decides to wait until the battle is over. Rayquaza flies above Groudon and Kyogre, at which point Ruby jumps off it. With the power of Rayquaza and the Red and Blue Orbs in hand, Ruby sends both Pokémon flying off Sootopolis City. Groudon and Kyogre, now calmed down, immediately leave to continue their long slumber.
With the battle finally over, Ruby tries to apologize to his father about everything he's done. To Ruby's confusion, Norman just stands there, motionless and unresponsive. On top of Registeel, Wallace celebrates with Steven over Ruby's victory. Steven tries to agree with him, but suddenly collapses. Ruby and Wallace try to shake Norman and Steven, but neither get a response. From the rubble of the Cave of Origin, two sets of eyes glow from within.