Zinnia charges for Ruby and Sapphire as they ride on Rayquaza's back, intending to knock them off. Sapphire sends out Rara and Kirly to protect the two from the attack. After Zinnia yells out a command to ignore Gardevoir and Gallade, Ruby realizes that Zinnia is fighting with another Pokémon. Ruby tells Rara to use Misty Terrain as Salamence prepares to use Dragon Pulse. Rara and Kirly are then struck by a powerful Boomburst attack, rendering them unconscious.
The two look up to see a Noivern above them, and for a moment, Sapphire believes she sees someone riding it. When Rayquaza begins to chase Noivern, Zinnia tells Ruby and Sapphire that Aster's spirit is present. She claims that Rayquaza is able to sense her, which is why it is following after Noivern. Ruby is shocked to learn that Noivern previously belonged to Aster.
While Rayquaza rapidly chases Noivern through the sky, Ruby and Sapphire struggle to hang on. Noivern leads Rayquaza straight toward Salamence as it prepares an attack. As Sapphire watches in horror, Salamence strikes Ruby with a powerful beam, knocking him off of Rayquaza. Sapphire screams Ruby's name, then sprints down the length of Rayquaza. As Ruby falls, he realizes that Sapphire has regained her voice. Sapphire leaps from Rayquaza's tail and grabs onto Ruby's hand.
Zinnia smiles, happy to be alone with Rayquaza at last. She kneels down on her Salamence, announcing to Rayquaza that she is the next Lorekeeper of the Draconid people. Zinnia requests for it to form a bond with her. Rayquaza responds by impaling her with its tail. Wheezing, Zinnia continues to plead for it to join her, but it blasts her with an attack that sends her plummeting through the air.
Later, as he rides on Latias, Emerald is relieved to see Ruby and Sapphire safe on Troppy's back. He reveals that Rayquaza is restlessly flying in the skies above Sootopolis City, and wonders if he can use his E Shooter with some mud from Meteor Village to calm it down. Sapphire asks about Zinnia, and Latias tells her that Latios rescued her and brought her to Sootopolis.
The group lands in the city to find Zinnia lying unconscious on the ground. Steven and Mr. Stone run up to Zinnia as she begins to wake up. Believing that the two are going to mock her, she is surprised when Mr. Stone apologizes. Bowing to Zinnia, Mr. Stone offers a lengthy apology to her, taking responsibility for the incident at the Embedded Tower, as well as the Devon Corporation's poor treatment of the Draconid people. Zinnia rejects his apology, believing that he only is saying it to make himself feel better. She tells him that he hasn't changed after the event at the Embedded Tower, which is proven by the fact that he was willing to randomly warp away the meteor without consideration of how it could damage another life-supporting planet. Through tears, she accuses Mr. Stone of never thinking about anyone but himself. She reveals that after Aster passed away, she wanted to give the Draconids hope that the world could be saved, even if she wasn't like Aster. Zinnia suggests that the Draconids were right to reject her as Lorekeeper.
Emerald speaks up, scolding Zinnia and Mr. Stone for accepting their fates. Despite their failures, he urges them to not give up. Emerald encourages everyone to do what they can to prevent the world from coming to an end.