Sitting by a fire, Red, Blue, Green, Bill, Ultima, and the Sailor camp out for the night. The Sailor holds a radio the broadcasts a message stating the current status of Five, Six, and Seven Islands. After consulting with Bill, Blue confirms that in addition to its first two formes, Deoxys has two more, making it a total of four. Bill goes on and states that when Red was almost defeated, Sird showed up on Five Island.
In a flashback, seeing Sird causes Bill to realize that she defeated Lorelei, but Sird states that the battle wasn't even a warm-up. Sird berates Carr for not defeating Red and states that they'll return to Seven Island after seeing Deoxys's last Forme. Sird tosses the two stones at Deoxys, which gives its half-transparent form full color. Sird dubs the stones the Ruby and Sapphire, which contain the climate of Hoenn. Sird uses the Ruby and Sapphire to turn Deoxys into its last Forme. Deoxys turns into a thin Forme that quickly flies past Red, knocking him over. Sird names this last transformation the Speed Forme, which maximizes Deoxys's speed. Afterward, Sird and Carr leave in pursuit of Deoxys.
Back in the present, the Sailor wonders how they can defeat their opponents. Blue states that it's not the first time they have face an opponent as strong as Deoxys. Blue suggests looking for Lorelei in the daytime and tells Red that they should go to Seven Island in the daytime. When Red doesn't give a response, Blue asks him what's wrong. Red gets angry at Blue and claims that he only said those things because he never had to fight Deoxys. They get into a brief fight, but Red states that he will understand if he fought Deoxys as well.
Blue suggests that they will have a chance if they work together to fight Deoxys, but Red states that they will still lose. Blue asks why Red became a coward. Red states that he is a coward, which he assumes is why the Pokédex was taken from him. Red notes how he had become so used to the Pokédex, he became dependent on it. He states that because of the Pokédex, he and the others had become famous, but was treated horribly when the people saw that he didn't have it.
Red claims that without the Pokédex, he is nothing, and that Professor Oak must think that he's no longer qualified to own one. When Red runs off, Bill tries to stop him only for Blue to tell Bill to let him go. Although Green ran after him, Blue tells them that they have more important matters to discuss. Blue reveals to everyone that Team Rocket has his grandfather, Professor Oak, in captivity.
Elsewhere on Five Island, Sird and Carr make their way to their base, the Rocket Warehouse. After entering the password, Sird begins looking for Deoxys on her computer. Elsewhere, an ! and ? Unown spot Deoxys landing on an island. Sird calls Giovanni and informs him that Deoxys has returned to Birth Island. After turning back into its Normal Forme, Deoxys becomes encased in a pyramid-shaped barrier, which Carr calls the Delta Shield. Carr notes that although Deoxys managed to win against Red, it still took a powerful Thunder to its core, which means that it needs time to heal.
Since Deoxys has been heavily injured, Giovanni tells Carr and Sird to leave Deoxys be for now. Carr notices a photograph that has been left behind. The photograph shows a younger Giovanni with a young, red-haired child being held in his arms. In his head, Giovanni notes how he will finally be able to see his son again.