B1F
Walk down the stairs, and you will find yourself in Team Rocket's underground base. Be aware of the Pokémon statues lining the northern wall. Each one has a hidden camera that will alert two Rocket Grunts to attack you, and each pair of Grunts will have the same Pokémon.
Rocket Security
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Trainers with a telephone symbol by their names will give their Pokégear number to the player, and may call or be called for a rematch with higher-level Pokémon.
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Walk to the west, and just before the second statue is a break in the southern wall. Continue south until you battle Scientist Jed. Pick up the X Accuracy behind him, and inspect his computer to deactivate the security cameras. Now you won't be ambushed by any more Grunts! Head out of Jed's room and walk east, where you'll find a Hyper Potion on the ground. Follow the hallway south from here, and then west. There is a Nugget halfway along the south hallway, and the stairs are in the southwest corner.
Team Rocket
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Trainers with a telephone symbol by their names will give their Pokégear number to the player, and may call or be called for a rematch with higher-level Pokémon.
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B2F
On the next lower floor, you will see Lance waiting for you, where he heals your team before running off. Battle past the two nearby Rockets, and take the stairs to the basement.
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Trainers with a telephone symbol by their names will give their Pokégear number to the player, and may call or be called for a rematch with higher-level Pokémon.
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B3F
Lance approaches you, saying that there are two passwords needed to reach the boss. Grab the Protein along the east wall, then head west through the southern area. Beat the scientist near the stairs, and battle the red-haired grunt just north of here. After defeating her, she gives up the first password: "SlowpokeTail". One down, but it's useless without the second. Leave this room and head west, battling Scientist Mitch on your way. Past Mitch is another Rocket, and this one knows the other password: "Raticate Tail". Grab the Dire Hit and Full Heal nearby, and head north. Pick up the Ice Heal, and head up the stairs in the northeast.
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Trainers with a telephone symbol by their names will give their Pokégear number to the player, and may call or be called for a rematch with higher-level Pokémon.
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B2F
Walk to the west along the north wall, and you'll be challenged by another Rocket. Head down the stairs, and you'll be near the boss's room. When you approach, your rival appears, insisting that he is the one who will eliminate Team Rocket. Take the south set of stairs to get TM46 (Thief), then enter the two passwords at the boss's door. The Rocket executive here talks about Giovanni disbanding the group three years ago, and how the organization has lingered since then, formulating plans for his return to command. After defeating him, he runs off to warn the others that their plans are in trouble. Talk to the Murkrow here to learn a third password, "Hail Giovanni", for the generator room.
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Trainers with a telephone symbol by their names will give their Pokégear number to the player, and may call or be called for a rematch with higher-level Pokémon.
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Backtrack to the generator room, where Lance healed your Pokémon. After entering the password, you get ambushed by two more grunts, who are looking to have a 2-on-1 battle. Their trick is short-lived, since Lance shows up with his Dragonite. You each battle a Rocket, and they run off, claiming that their experiment was a success regardless of their defeat here. Lance inspects the large generator, and you each have to defeat (or capture) the three Electrode on each side of the machine in order to shut it down. With the machine disabled, Mahogany is finally rid of the Rockets, and Lance rewards you with HM06 (Whirlpool). Follow him up the stairs, and take the warp tile back to the entrance.
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Trainers with a telephone symbol by their names will give their Pokégear number to the player, and may call or be called for a rematch with higher-level Pokémon.
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Now you can challenge the Mahogany Gym!