How to Get the Wailmer to Move in Lilycove City on "Pokemon Sapphire"by Mitch Reid ; Updated September 22, 2017
In “Pokemon Sapphire,” your adventure across the Hoenn region will require you to traverse routes from city to city. However, your journey won’t always be straightforward. In some cases, obstacles will block routes until you complete certain events in your current location. For example, as you try to sail east from Lilycove City, Wailmer, a Pokemon that resembles a whale, will obstruct your travels. The Pokemon will only move after you have infiltrated Team Aqua’s nearby base.
Travel to Slateport City, a community in the southern Hoenn region. Visit the harbor on the east section of the city. Once you arrive, you will discover that Team Aqua has stolen a submarine from the port.
Go to Lilycove City in eastern Hoenn. Use Surf to travel northeast from the beach until you find the cave that serves as Team Aqua’s hideout. If you overshoot the cave, you will run into the barricade of Wailmer.
Enter the cave and head for the door in the northeast corner of the entrance room. In the next room, step on the warp pad to your left. It teleports you to another room.
Walk to the right, passing several tables, until you reach another warp pad. Warp to a new location.
Enter the door behind you in the next room. Step onto the warp pad on the right side of the following room.
Walk through the next doorway, which is to your north. In the next room, pass between two tables to reach a doorway on the other side of the room.
Step onto the next warp pad, which is to your south, to teleport into a room with a submarine. Defeat the Aqua Admin standing guard near the submarine. The Admin will use three Pokemon at level 32. After the battle, the submarine will depart.
Use the next warp pad to leave the Aqua Hideout. Outside of the cave, Wailmer will have departed also.
Explore every section of Team Aqua’s base to uncover rare items, such as a Nugget and a Master Ball. Expect to battle several Team Aqua Grunts as you walk through the base. Their Pokemon will be around level 30.