Emerald stares at Jirachi after making his wish. He looks at the statue of his seniors, which haven't changed at all. Although he wonders why nothing has changed, Emerald realizes that he needs to look at Jirachi's third eye. Emerald asks Jirachi to open its third eye, but it floats away from him. Emerald begs Jirachi to tell him why it would grant a wish of someone as evil as Guile Hideout instead of him.
Elsewhere, Crystal, Ruby, and Sapphire leap off of the edge of the Battle Tower. They suddenly land on an invisible floor, which Crystal reveals that she had created with her Mr. Mime, who used its ability to solidify air. Crystal reveals that she had gotten the idea after watching Sabrina's battle against Bugsy. They head down the stairs into a room below.
When Ruby asks why she created rooms, Crystal gives him and Sapphire each a bracelet. Crystal tells them that their goal is to learn the ultimate moves Hydro Cannon and Blast Burn. In addition to the ultimate Grass-type move, the bracelets were given to them from Ultima of Two Island. Crystal tells them that they have to learn the moves right away in order to stop the monster Kyogre. Ruby suggests that since Kyogre is a Water-type Pokémon, they should use Grass- and Electric-type moves.
Crystal explains that the monster Kyogre isn't a Pokémon, but a giant cluster of energy, which can only be defeated by an equally powerful blast. Crystal notes that when Latios used Luster Purge, it managed to cut through the Kyogre, leaving a permanent hole in its fin. Ruby and Sapphire, having fully understood what they have to do, accept their mission. Crystal leaves to join the team tasked with distracting Guile.
While Crystal and the other flying Pokémon attack the Kyogre, Emerald tries to figure out why Jirachi didn't grant his wish. Gold tells him that he's lacking in determination. Gold shows him Pika and Chuchu, who managed to escape being petrified by being out of their Poké Balls at the time. He states that they came all the way to the Battle Frontier because they had faith that their Trainers would be cured. Gold jumps onto Tibo's back and tells Emerald that everyone is counting on him as he flies away to join Crystal. He tells Emerald to join Ruby and Sapphire in learning the ultimate moves.
While Gold, Crystal, Latios, and Troppy battle Kyogre, Emerald jumps down and joins Ruby and Sapphire. Sapphire greets Emerald and hands him the bracelet. Ruby states that in order to learn the techniques, they will have attack the Pokémon that is weak to a certain type. Mumu, Chic, and Sceptile launch their attacks, but Sceptile gets hurt more than usual because Emerald keeps spacing out. Emerald states that he's in shock after being rejected by Jirachi and can't concentrate on anything else.
Ruby and Sapphire suggest Emerald tell them more about himself since they don't know him well enough to know how to cheer him up. Emerald takes off all of his gadgets, revealing how short he truly is to everyone. Emerald guesses that they're shocked, but states that's how he truly is. Emerald claims that he's always been alone.
In the Chuang Yi version, the Fire type is mistakenly called the Flame-type.
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