When you arrive in Slateport, head straight for the northeast part of town. Outside Slateport Harbor, you find Captain Stern wrapping up a TV interview in front of a small crowd. Afterwards, you catch up with him for a little chat where he informs you of his newest discovery. He's found an underwater cavern on Route 128, and believes it to be the den of a super-ancient Pokémon long though to have been extinct. Just then, you hear a voice booming out from a megaphone. It's Archie, who mocks the captain and thanks him for the submarine.
After rushing inside the building, you find Archie and a Grunt standing near the sub, ready to depart. He accepts that you won't simply leave him to his plans, and wonders if you will visit their hideout in Lilycove City. But he's come too far to be stopped now, and he and the Grunt quickly escape in the sub.
Members of the Pokémon Trainer Fan Club discuss popular Pokémon Trainers and Gym Leaders. After entering the Hall of Fame, several members announce themselves as your fans, as well.
Cove Lily Motel
Team Aqua's hideout on the edge of town has kept most tourists away, bringing the Cove Lily Motel's business to a halt. As a result, there's nothing of interest here at the moment. After resolving the conflict with the villainous team and entering the Hall of Fame, the Game Freak staff will visit the motel during their trip to Hoenn. The Game Designer will give Trainers the Poké Diploma after completing the Hoenn Pokédex.
Scott can be found here on the upper level, but he only appears before Team Aqua steals the submarine from Slateport City.
Pokémon Contest Hall
The Contest Hall stands on the south side of town. This building hosts all four Contest levels—Normal Rank, Super Rank, Hyper Rank, and Master Rank. A receptionist will give you a Pokéblock Case, which lets you enter the Safari Zone north of Route 121, if you talk to her. Several powerful Pokémon, such as Girafarig, Pinsir, and Heracross, are found in the Safari Zone and nowhere else.
Pokéblock Master's House
The Pokéblock Master's house stands to the north of the harbor. Talk to her and her family to learn tips on crafting potent Pokéblocks.
Rival Battle 5 (optional)
When you approach the Department Store, you find May/Brendan waiting outside blocking the entrance. She/He offers to battle you to determine which Trainer has been doing a better job of raising their Pokémon in a fifth and final battle.
Once the battle ends, your friend heads back to Littleroot Town to continue working on her/his Pokédex.
Lilycove Department Store
Welcome to the Lilycove Department Store! This massive shopping center offers a wide array of merchandise, so Trainers can find almost any item for sale here.
1F: Service Counter, Lottery Corner
The first floor is a welcome center. The receptionist on the left greets visitors, while the one on the right runs the Pokémon Lottery Corner. Talk to her to draw a random Pokémon Loto Ticket. If the ticket's number matches up with any of your Pokémon's ID numbers, you win a prize! You can draw one Loto Ticket per day.
The fifth floor is dedicated to Secret Base fanatics. Here you'll find a wide selection of Decorations to deck out your Base, including dolls, mats, posters, and cushions.
After entering the Hall of Fame, the store occasionally holds a major clearance sale. A special selection of Secret Base Decorations are offered, with items listed anywhere from 200 to 10,000. Though this sale rarely occurs, many of the items available for purchase cannot be obtained anywhere else.
Also on the rooftop, a girl fantasizes about copying herself and living several different lives. Speak to her, and she offers to teach the move Substitute to a Pokémon, one time only.
The Lilycove Museum stands in the northwest part of town. The museum's curator initially blocks the stairs to the second floor because the upper level is empty. He is still searching for modern and vibrant artwork to display there, and asks you to search for such artwork. If you happen to win a Master Rank Pokémon Contest with at least 800 points, an artist will approach you saying that he's done a painting that might even look good in a museum, at which point you direct him to the Lilycove Museum. If you collect one painting for each of the five Contest categories, the curator will reward you with a Glass Ornament for your Secret Base.
Move Deleter's House
The first house to the east of the Department Store is home to the Move Deleter, an absent-minded man with the power to make a Pokémon forget any move. This is the only way for a Pokémon to forget an HM move. Unlike the Move Reminder in Fallarbor Town, the Move Deleter's services are free of charge.
A Berry A Day
Speak to the Gentleman to the east of the Move Deleter's house to get one random Berry from a group of ten every day.
Team Aqua has been working hard to build an impressive hideout in this spacious cave to the northeast of Lilycove's beach. You'll need to storm their hideout in order to retrieve Captain Stern's submarine and prevent Archie's misguided vision from becoming reality! Bring a party that can handle plenty of battles against them. When choosing your team, remember that Team Aqua often uses Water- and Dark-type Pokémon.
Climb out of the water and up the stairway. At the top, a single Aqua Grunt patrols around the pool of water. Battle him and head down the stairs to the northeast.
There are two warp panels in the northeast room; take the eastern panel first to reach the east-central room and a Max Elixir. Warp back and take the other to reach the northwest panel in the southern room. Ignore the three Aqua Grunts and take the warp panel in the southwest.
The previous warp panel leads to a small room with several more. Follow them in the correct order—left, center, left, left—to reach the interior room on B1F.
In Archie's office, you'll find four items near the far wall. Two of them are actually Electrode in disguise, while the bottom-left item is a Nugget and the top-left item is a Master Ball! This type of Poké Ball will catch any wild Pokémon without fail, and is best used on hard-to-catch legendary Pokémon. Backtrack through the warp-filled hallway to B1F's southern room, battle the three Grunts, and step on the southeast warp panel. This transports you to the north-central room; head down the stairs to B2F.
Go south and step on the warp panel there to be transported a short distance to the west; collect the Nest Ball from this enclosed area before warping back. Head northeast past another patrolling Aqua Grunt and take the warp panel there to the northwest room. Climb the stairs back to B1F.
Battle past the single Aqua Grunt here and head down the stairs to the northeast.
Battle the two Aqua Grunts and step on the warp panel to the southwest; this leads to the southeast corner of B2F. Go west to find one of the Aqua Admins, Matt, standing at the water's edge. He's the only thing standing between you and stopping Archie's getaway!
The battle lasted just long enough for Archie to escape in his souped-up submarine. You've got to chase after him to the Seafloor Cavern, but you have no means of diving underwater like he can in his sub. For now, you'll have to keep to the surface. Head south then east and take the warp panel there back to the cave entrance and Lilycove City. The Grunt and his Wailmer blockade have disappeared from the beach, leaving you free to venture out into the eastern ocean.