Inside the rampaging TR battle airship, Red decides to stay behind on his own to deal with the failing aircraft, and the black hole created by Deoxys slowly swallows up Mewtwo and Yellow, despite their protest. However, before she gets completely engulfed, Yellow does a last minute struggle, and tells Red to wait as she swings her fishing rod out. The fishing line catches Red by his left little finger, and Red, who is taken by surprise, sees that the other end is coiled around Yellow's own same finger.

The blasted hole on the battle airship's right side causes severe imbalance to its flight, and the aircraft spins on its own uncontrollably as it soars across the skies of Kanto. At Fuchsia City, the warden of the Safari Zone and his mecha-pidgey hear the defeaning sounds of engine, and look up in horror to see the broken giant aircraft giving out thick clouds of black smoke. The warden's astonishment causes him to spit out his fake gold teeth, and his mind boggles with fear that the aircraft is about to crash. However, the aircraft manages to speed past Fuchsia, and mecha-pidgey hollers that it is heading for Vermillion.

At the Vermillion harbour, the President of the Pokemon Fan Club and his club members soon spot the failing aircraft approaching their city as well, and cry in terror that a big tragedy is about to happen.

Meanwhile, the speedy liner Sea Gallop has just returned from the Sevii Islands, and the sailor announces that they have successfully docked. Everyone on board looks up from the deck to see the midair terror, and Brinca wonders if it is Team Rocket's battle airship. Green is certain that it is the very enemy aircraft Red and Mewtwo chased after, and Blue switches to the news channel on her Pokegear to discover that there is already coverage on the incident.

The reporter states that the giant airship began losing control over the skies of the Viridian Forest, and after soaring above Fuchsia, is now going haywire right on top of Vermillion. Blue rationalizes that after Red and Mewtwo reached the aircraft and fought Deoxys, something must have happened. She turns to Lorelei and asks if the Beast Warrior Trio are on the aircraft, but Lorelei finds no signal on her compact mirror tracer, and remarks that at least Storc isn't on board.

Green then tries to contact Red with his Pokegear, but the call fails to go through. Green grunts that Red seems to be outside the signal coverage zone, but regardless of who is on board the aircraft, from its current state, it shall lose control completely and crash at any moment, and the one thing they should do right now is to limit its scope of destruction. With that, Green and Blue jump off the Sea Gallop, and dash towards the city center.

Back on the TR battle airship, Yellow clutches tight onto her fishing rod, and struggles to keep herself from being swallowed into the black hole. Inside the Pokéball attached to the end of fishing line which is coiled around Red's little finger, Chuchu spots Pika in its Pokéball on Red's belt, and the two Pikachus are surprised to see each other.

Red wants to know what Yellow is doing, and the girl explains that she has something important to tell Red. It turns out that before she fell victim to her sleep attack, she managed to fully comprehend what Deoxys was trying to say, and she finally understands that the reason why this Deoxys named Individual 2 claims to be Red, is because Red's blood flows in its body.

Red is stunned speechless momentarily at the statement, and wonders how is it possible. Yellow explains that in order to obtain greater battling power to further his evil deeds, Giovanni has collected various cell samples and energy sources over the years. Amongst them, it contains Red's blood sample. Five years ago, in Red's battle with Giovanni at the Viridian Gym, both trainers were wounded. At the end of the battle, Giovanni secretly took some of the fallen cement splashed with Red's blood away, and kept it as a sample.

Afterwards, when Deoxys Individual 2 broke free from Team Rocket during its ethereal stage not long ago, it caused havoc at the storage room, and incidentally absorbed Red's blood sample which was kept there. Being a mutated space virus, Deoxys doesn't have a home nor a family. Its innate nature thus regards Red as its own roots, and yearns to find and meet him. Unfortunately, at that time, the only means of communication Deoxys knows of is to attack and battle, which explains its aggressiveness towards Red upon their first encounter. As for the special feeling Red experiences whenever Deoxys appears, it is perhaps a calling from Red's own blood which is flowing inside the body of Deoxys.

Having explained Deoxys's message to Red, Yellow quickly finds herself getting another sleep attack. As she losens her grip on the fishing rod, the fishing line around her little finger slowly uncoils. She is grateful, however, that she has delivered the message fully, and that Silver is also being warped to a safe place, which means her task there is complete. With that, the young trainer falls asleep and slips into the black hole, leaving just her straw hat, the fishing line, as well as Chuchu's Pokéball behind.

Red remains wordless for a moment as he thinks over Yellow's words, then turns to Deoxys, and says he is glad that he finally understands what it means. He recalls what Yellow said about battling being Deoxys's only means of communication, and muses that his blood must have carried his combative trait to Deoxys as well. Deoxys stares with Red with a baffled face, and Red quickly apologizes for saying funny things.

The boy then looks over to the pilot seat, and climbs up to attempt steering the aircraft into control. He tells Deoxys that he is honoured, however, to be the one person whom such a strong and diversely skilled being seeks. Red states that although Deoxys has been captured by Giovanni and is technically the man's Pokémon, it is now free and can choose to go back to the wild. However, it can also choose to stay behind and fight alongside with him, let him show it what friendship is, and what it means to be companions.

With that, Red sends out Poli, Lax, Gyara, Aero, Charizard, Pika, as well as Chuchu, and gets ready to collaborate once again with his trusted companions. With his hands on the steering handle, he admits that he has never controlled any vehicle aside from a bike, but he will do his best. While he stays in charge of the pilot position and makes sure the aircraft doesn't crash, everyone else should try to locate the remaining Forretresses and faint them.

The Pokémon are about to take off when Red notices a message on the monitor screen telling him to wait, and that it will help him locate the Forretresses. Red realizes that it is Deoxys talking to him, and tells the others to follow its directions. Closing his eyes, Deoxys swiftly detects the whereabouts of the Forretresses with its psychic powers, and displays his thoughts as letters on the monitor screen.

Near the right engine rotor, Poli soon finds the first Forretress there and faints it with a hydropump. On the second floor of the central cabin, Gyara knocks out the second one, while Pika and Chuchu electrify the third one with their combined thunderbolt in the store room in the basement. As long as they manage to keep working at this pace, Red believes that there might just be a chance that he will succeed…

Thanks To Coronis For Writing this for us