In the Pokémon Tower, Red calls out to Blue, but quickly realizes from the latter's eyes that his rival is being controlled by the mysterious fog of the Tower. While Saur fights the possessed Blue and his Charmeleon, Red deduces that Blue is being controlled by a Gastly and tries to stop it by having Saur use Razor Leaf. Due to Gastly's gaseous body, the attack simply goes right through, and Charmeleon gets ready to subdue Saur with a massive Fire Spin attack. Quickly, Red has Saur use the bulb on its back to suck in the Gastly and the fog it created, freeing Gastly's possessed victims before expelling Gastly in a Solar Beam.
Red rouses Blue from his stupor, but much to Red's surprise, Blue heads further into the Tower, determined to find the individual responsible for turning him into a mindless slave. On the way up Red barely avoids touching the corrosive venom from a Poison Pokémon, and at Blue's demand, the culprit reveals himself to be Koga; an elite agent of Team Rocket. Koga reveals that Team Rocket had been using the Tower as a base of operations, and thanks to the townspeople fear of the Tower they had managed to carry out operations undisturbed. Blue has his Charmeleon attack Koga; however, it proves to be only a projection, with the real Koga controlling his Pokémon from elsewhere.
Koga sends his Arbok after Red and Blue, who quickly unleashes its corrosive Acid. The boys run back to where Red had encountered the zombies, and Blue orders a Reflect from Charmeleon. Outside the tower Koga observes the battle from a Golbat-shaped screen, and commands another Acid that appears to break past Charmeleon's defense and corrode it as well. Koga gloats at his victory, but is soon surprised as Charmeleon slices Arbok cleanly in two. Blue explains that Arbok had instead melted the Psyduck corpse from earlier, and points out that Koga's strategy of controlling his Pokémon from a distance meant that he couldn't see through the substitution ploy. Red silently concedes Blue's skill while Koga, crushing his screen in anger, swears vengeance on the two boys.
Sometime later, Mr. Fuji thanks Red for restoring life back to Lavender Town, and for giving his deceased Doduo a proper resting place, but Red modestly credits Blue for what happened. As he watches Blue depart, Red continues on his journey.
This was the last round of the manga to be translated into Polish.
When Red encounters Koga, Koga states that, "...You'd think that an Evil Crime Syndicate could built a simple base...". Koga meant to say either "...could have built..." or "...could build..." instead.
In the Japanese version, Red thinks about the crowd of undead Pokémon while seeing Koga's Arbok that was split in two pieces by Blue's Charmeleon. In the Chuang Yi version, this was changed to Red thinking "Oo. This Blue is good. Not that I'll ever tell him that..."