| It All Ends Now I/The Final Showdown I
|Spoiler warning: this article may contain major plot or ending details.|
Upon seeing the scar on his forehead, Sapphire learns that Ruby is the boy she met when she was younger. A voice appears, and asks if Ruby is finished. The voice is revealed to be Courtney, who had come to help. Ruby, with both Orbs in hand, flies on Troppy towards Groudon and Kyogre with Courtney. Sapphire, locked inside Wallace's aircar, watches in horror as Ruby and Courtney fight Groudon and Kyogre.
Wallace, watching the battle on top of Registeel wonders why Ruby trapped Sapphire in his car and is fighting with a woman from Team Magma. Wallace, having put is trust in Ruby and Sapphire and called Juan to train them, wonders what is going on in Ruby's mind. Steven snaps Wallace out of it, and points out that they have to get Sapphire out of the aircar immediately.
On top of Regirock and Registeel, the Elite Four comment about how Groudon and Kyogre never seem to get tired. Drake notes that with the power of Regirock, Regice, and Registeel, the power erupting from Kyogre and Groudon is being contained. However, Glacia and Phoebe note that the power continues to increase, and with nowhere to go, it rises up into the sky.
As Ruby dodges the debris being sent up by the energy created by Groudon and Kyogre, he wonders if his decision was the right one. In his head, Ruby notes that he's surprised that not only could a nice girl like Sapphire actually like someone like him, but Sapphire is the girl he knew when he was younger. Courtney appears next to Ruby, and berates him for not focusing, which could end in his death. Ruby apologizes to Courtney and admits that he'd never thought he would fight together with her.
In a flashback to Mirage Island, Ruby tries to get his malfunctioning Pokédex to work. Suddenly, it begins to work again, and has been filled with the records of Sapphire's adventures. Ruby realizes that their Pokédexes must have been connected to each other when they were knocked around by the attacks of Groudon and Kyogre. While Sapphire sleeps, Ruby reads how much Sapphire had traveled on foot compared to how he had been moving around by car throughout his adventure.
Suddenly, a flame appears in darkness, which is revealed to be Courtney. Ruby immediately sends out Mumu to defend himself and demands to know why she's there. Courtney reminds Ruby that she had promised to follow Ruby everywhere he goes, no matter the cost. Ruby quickly realizes that when Tate and Liza sensed the presence of someone else, they sensed Courtney, not Plusle and Minun. Courtney gives Ruby the offer to team up and stop Groudon, shocking him.
When Ruby questions her motives, Courtney reveals that even though she helped free Groudon to increase the land, the entire thing has gone far beyond what Team Magma and Aqua had intended. Because there's no point in anything if Hoenn is destroyed, Courtney considers her and Ruby on the same side. Courtney reveals that she knows that Ruby and Sapphire are undergoing training to control the Orbs, but proposes the idea of what would happen to Sapphire if she lost control. As Ruby imagines a possessed Sapphire, he reluctantly accepts Courtney's offer.
Back in the present, Courtney notes that Ruby must really like Sapphire if he accepted her offer so quickly. Courtney expresses some jealousy at Ruby's caring of Sapphire, which confuses Ruby. Ruby hands Courtney the Blue Orb and the two prepare to end the battle.
- Ruby goes out to fight with Courtney.
- Due to the energy of Kyogre and Groudon being trapped, it slowly rises to the sky.
- The reason why Ruby teamed up with Courtney is revealed.