As the battle between Groudon and Kyogre continues, the energy created by their battle forces Sootopolis City and the earth surrounding it to rise up into the sky. The HoennElite Four, as they watch earth rise, wonder what is going on in the city. As the energy grows between Groudon and Kyogre, Ruby and Courtney stand before them in front of the Cave of Origin. The two present the Red and Blue Orbs and command Groudon and Kyogre to end their battle.
The two Pokémon ignore the Orbs, which annoys Courtney. They decide to attack their opponents to get their attention, so Ruby sends out Mumu while Courtney sends out her Ninetales to attack Groudon and Kyogre. Their attacks have no effect, so Ruby comes up with the idea to attack their stomachs, as those aren't nearly as protected as their backs. The idea works, and Courtney notes that Ruby had become stronger since their last battle at the Rusturf Tunnel.
Ruby notices that the area they are currently in is the same place where he and Sapphire had used the Grand Meteor on the Red and Blue Orbs earlier. This distracts Ruby, which causes the energy of the Red Orb to be rebounded into his arm. Courtney tells Ruby to not get distracted, but doing so causes the Blue Orb to do the same to her body. Courtney regrets her lecture of Ruby, but decides to take this opportunity to try and control Groudon and Kyogre again.
They attempt to control the rampaging Pokémon again, which manages to get their attention. Immediately, the two begin attacking Ruby and Courtney in an attempt to stop them before continuing their battle. With Mumu's Endeavor, Ruby manages to knock Groudon away and on top of Kyogre. Kyogre attacks, but Courtney pushes Ruby out of the way, which causes pieces of the Cave of Origin entrance fall on top of her.
Ruby tries to help Courtney, but Groudon pins him to the ground before he can get to her. Courtney claims that they failed, but she isn't surprised as she wasn't chosen by the Orbs. Suddenly, Courtney, Groudon, and Kyogre, notice a figure in the sky quickly approaching them. The figure is revealed to be Rayquaza, which flies over Sootopolis.
When Ruby asks what Pokémon it is, Courtney reveals that Rayquaza is the third ancient Pokémon of Hoenn that is rarely talked about. Rayquaza immediately begins battle with its fellow ancient Pokémon, surprising Ruby. Courtney, in her mind, reveals that she noticed a figure on top of Rayquaza's head earlier.