As Mewtwo sinks down into the black hole with Yellow, it asks Red what he plans on doing. Suddenly, a fishing line shoots out from the black hole and surrounds Red's hand. The culprit is revealed to be Yellow, who used her fishing pole to pull herself back up. Yellow states that if she leaves now, she won't be able to tell Red the whole story of Organism No. 2. Since she will be falling asleep from overusing her powers, she'll have to tell Red what she saw in Organism No. 2's mind.
Yellow reveals that Red's blood flows inside Organism No. 2's body. Yellow states that in order to strengthen his forces, Giovanni collected various cell samples. One of the samples was the blood Red left behind after their battle in Viridian five years ago. When Organism No. 2 escaped from Team Rocket's custody, it must have absorbed Red's blood into its system after going on a rampage in Team Rocket's vault.
Since the two Deoxys had no family, Organism No. 2 thought of Red as its ancestor and sought after him. But back when it first appeared, Deoxys could only communicate by fighting. Red realizes that the sensation he felt every time he saw Organism No. 2 was his blood calling out to him. Yellow, unable to keep her eyes open, states that she's glad she was able to give Red the information in time. Yellow is then fully absorbed by the black hole, causing her fishing line, with Chuchu's Poké Ball attached, to break off the fishing pole.
Red tells Organism No. 2 that he now understands what it meant by stating that it is him. He claims that Organism No. 2's communication did shake him up, although he states that he was only kidding. Red hops into the pilot's seat and grabs the airship's steering wheel. Red tells Organism No. 2 that he feels honored that someone needs his help, no matter what form they're in. Red notes that although it was captured by Giovanni, he gives it the offer to leave Giovanni or even join his team. Red tells Organism No. 2 that now that they have had a battle, they're friends now.
Red sends out Poli, Gyara, Snor, Aero, Charizard, Pika, and Chuchu. Red notes that he's only ridden a bicycle before, so he will have to pilot the airship by imitating what he saw before. He tells the Pokémon that he will handle piloting the airship while they will have to take care of Carr's ten Forretress. Suddenly, text appears on the computer in front of Red, which is revealed to be Organism No. 2 using its psychic powers. With Organism No. 2's help, Poli, Gyara, Pika, and Chuchu locate the first three Forretress and defeat them.