After Silver notices that Lugia isn't inside the Poké Ball, they think about how and when Lugia could have escaped. Crystal finally realizes that it must have flown off in the flash of light. Gold stomps about in frustration when Crystal remembers the tracking system on the Pokédex, which can track the energy of any Pokémon the Pokédex holder has encountered.
Crystal then asks Gold and Silver if they had heard of the feature before, but they say nothing and pretend to know how to use the system, Gold looks over Crystal's shoulder as she activates the system on her Pokédex and mimicks her actions. Gold apparently offends their new acquaintance by telling her that she is not merely a "motor-mouthed prissy girl." Crystal then introduces herself at last, but Gold ignores her, deeply involved as he is waiting for the tracking system to track Lugia. Ignoring both of his companions, Silver climbs up the island's crag and discovers a cave which, by virtue of the tracks before its entrance, he deems to be Lugia's lair.
Crystal recounts a legend that the four Whirl Islands are connected by tunnels and states that these would be a suitable hiding place for a gigantic Pokémon. Silver also sees signs of a struggle, and he and Gold suppose that Lugia might have been attacked before they encountered it. Crystals states that it would explain its rampage, but suddenly the tracking system crashes on all three Pokédexes. Realizing that it isn't likely that all three would fail at once, Gold states that the only explanation is that Lugia has already been captured by someone else.
Meanwhile, the S.S. Aqua is safe and sound again, swiftly cutting through the waves. A sailor aboard is relieved that he made it out of the attack, when Lt. Surge suddenly bursts through the door of the ship's control room, alive and unharmed. Just as Lt. Surge begins to reflect on his adventure, a letter comes in at the ship's bridge, which is a summons for Lt. Surge and all the other Gym Leaders to appear at the Pokémon Association headquarters in Goldenrod City.
Back on the Whirl Islands, Silver speculates that someone could have struck Lugia with a Poké Ball immediately before Crystal did. Silver then brings out his Murkrow, guessing that whoever attacked Lugia in the cave is the culprit and that the entire fight that they had with the Legendary Pokémon was a trap. Despite Crystal's objections that he should at least speak to Professor Oak and Professor Elm before chasing Lugia's captor, Silver flies off clutching Murkrow's talon. Gold assures Crystal that Silver would not call the Professors under any circumstances and, in spite of his old habit of warning Silver not to try to handle everything on his own, thinks well enough of this departure as he and Silver have a common enemy this time. Crystal begins to wonders what Gold could mean by that, but remembers Yellow and Wilton.
Suddenly, she gets a call from Professor Oak on her Pokégear. Professor Oak states that he is aware of the unusual events near Cianwood City and has called to check on Crystal. Crystal tells him about everything that has happened to her lately, including the part about losing Yellow. Oak informs her that there is a meteorological crew on the way, and he will tell them to look for Yellow. He also needs her to go to the Indigo Plateau, and says that he was also going to ask Gold to go, but has been unable to reach him and could be anywhere. However, Crystal reveals, he is standing right next to her.
Meanwhile, Silver flies high above the island chain and lands on the southernmost isle, which is the only one that he and Gold have not visited. Its crag houses a whirlpool and at the back of which is a roaring waterfall. Touching down, Silver sends out Gyarados, Kingdra, and Feraligatr and orders them to use Whirlpool, Waterfall, and Surf, respectively. Using Feraligatr, Silver sails over the calmed pool and steps through the parted fall into what appears to be a man-made chamber. From the darkness comes a voice affirming the place hidden to all except those with three Water-type Pokémon with a precise combination of talents. Lance then steps forward, congratulating Silver on reaching the chamber.