The next morning, Crystal heads to Union Cave to go to the west side of Johto. While traveling through the cave, she flashes back to Bill informing her that the same species from Kanto and Johto might look slightly different, and therefore Professor Oak would like her to collect them again. Back in the present, Crystal spots a Magneton, which doesn't live in the cave. Suddenly, three more Magneton appear and surround Crystal and Megaree, who then drop them in a submarine.
Afterwards, Lt. Surge approaches the submarine, but is disappointed to discover that it his Magneton didn't get any wild Pokémon. Lt. Surge then enters the submarine to travel to Azalea Town. He leaves through a secret passage, but gets stuck on a reef of Corsola. Crystal comes to and surprises Lt. Surge when he realizes she is on board. Briefing her on the situation, she figures out that she has to capture the leader. Natee creates a current with Psychic, which lifts them up. After they are out of the water, Natee defeats the leader with Psychic, which Crystal captures with a Lure Ball. As compensation, Lt. Surge gives her a ride to Olivine City on the S.S. Aqua.