This is the Bulbapedia walkthrough for Pokémon Gold and Silver. This walkthrough follows the original Game Boy Color version, not Pokémon HeartGold and SoulSilver.
The guide for those can be found here.
Mahogany Town
Mahogany Town is a small, quiet town in northern Johto. On your first visit, the Mahogany Gym is blocked off, and a man at the town's east end prevents travel to Route 43. There is no official Poké Mart here, but the shop in the center of town sells odd items (like TinyMushroom and SlowpokeTail) as well as the standard Poké Balls and Potions. With nothing else to do, head up north to the Lake of Rage.
Route 43
Route 43 stretches between Mahogany Town and Lake of Rage.
There are two paths to reach the lake. Traveling through the guardhouse will cost Trainers $1000, since a pair of Rocket grunts jumps you as soon as you step inside. The grassy trail alongside the pond is just as long, but doesn't require payment to pass. Whichever way you choose, continue north to the Lake of Rage.
Trainers
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Trainer
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Pokémon
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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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Available Pokémon
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Pokémon
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Games
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Location
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Levels
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Rate
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G
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S
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C
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15
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30%
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G
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S
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C
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15
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30%
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40%
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30%
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G
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S
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C
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15
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30%
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30%
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0%
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G
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S
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C
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17
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25%
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20%
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0%
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G
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S
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C
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16
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30%
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30%
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0%
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G
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S
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C
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16
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20%
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20%
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0%
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G
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S
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C
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15-17
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15%
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15%
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0%
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G
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S
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C
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15
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10%
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10%
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5%
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G
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S
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C
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16
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5%
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0%
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15%
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G
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S
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C
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15-17
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0%
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0%
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40%
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G
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S
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C
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17
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5%
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5%
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0%
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G
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S
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C
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16-17
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0%
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0%
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25%
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G
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S
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C
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17
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0%
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0%
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20%
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G
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S
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C
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16
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0%
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0%
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30%
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G
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S
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C
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17
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0%
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0%
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5%
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G
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S
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C
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10
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80%
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G
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S
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C
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10
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50%
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G
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S
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C
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10
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65%
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G
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S
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C
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10
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50%
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G
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S
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C
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10
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30%
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G
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S
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C
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10
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30%
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G
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S
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C
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10
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20%
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G
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S
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C
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10
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20%
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G
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S
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C
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10
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15%
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Surfing
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G
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S
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C
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15-24
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100%
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A colored background means that the Pokémon can be found in this location in the specified game. A white background with a colored letter means that the Pokémon cannot be found here.
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Lake of Rage
Once you reach the lake, save your game. Surf to the center to battle the red Gyarados. It isn't necessary to capture it, thought not a bad idea. After the battle, it drops a Red Scale; show this to Mr. Pokémon on Route 30 and he will give you an Exp Share.
Step onto the shore, and you'll see Lance reading the nearby sign. Speak to him to learn more about Team Rocket's plans, and head back to Mahogany. Visit the shop, and Lance will show you the entrance to the Rocket hideout.
Available Pokémon
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Pokémon
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Games
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Location
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Levels
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Rate
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G
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S
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C
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5-25
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90%
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G
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S
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C
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5-25
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10%
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G
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S
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C
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10
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100%
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G
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S
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C
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20
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90%
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G
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S
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C
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20
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10%
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G
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S
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C
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40
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70%
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G
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S
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C
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40
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30%
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Special Pokémon
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G
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S
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C
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Shiny
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30
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One
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A colored background means that the Pokémon can be found in this location in the specified game. A white background with a colored letter means that the Pokémon cannot be found here.
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Later...
Wander through the forest maze on a Wednesday, and you will run into Wesley near the house in the northwest. Speak to him to get a Black Belt, a power-up for Template:Type2s.
Rocket Hideout
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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Pokémon
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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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Trainer
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Pokémon
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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.
Team Rocket
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Trainer
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Pokémon
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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.
Team Rocket
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Trainer
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Pokémon
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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.
Team Rocket
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Trainer
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Pokémon
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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.
Team Rocket
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Trainer
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Pokémon
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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!
Mahogany Gym
MAHOGANY TOWN
POKéMON GYM
LEADER: PRYCE
The Teacher of
Winter's Harshness
Pryce is at home in the winter wilderness, and has installed icy tiles in his Gym to thwart all but the most determined Trainers. The Mahogany Gym specializes in Ice-types, so Fire-types (like Typhlosion) and Fighting-types will have an easy time here.
Mahogany Gym
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Trainers
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Trainer
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Pokémon
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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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After defeating him, Pryce gives out the Glacier Badge, which increases your party's Special Attack and Special Defense, and allows the use of Whirlpool outside of battle. Pryce also gives you TM16 (Icy Wind), symbolizing winter's harshness. One more badge to go!
When you step outside the Gym, Elm calls you about strange radio broadcasts that mention Team Rocket. It seems the gang won't take a hint, so fly back to Goldenrod to finally put an end to them.