This is the Bulbapedia walkthrough for Pokémon HeartGold and SoulSilver.
These pages follow the remade Nintendo DS iteration, not Pokémon Gold and Silver. The guide for those games can be found here.
Mahogany Town
Mahogany is a small, quiet town in the northeast mountains that connects Routes 42 to the west, 43 to the north, and 44 to the east. There is no official Poké Mart, but the Souvenir Shop in the center of town offers the usual Poké Balls and Potions in addition to oddities like TinyMushrooms. The east exit is blocked off by a man selling RageCandyBars. The Mahogany Gym is currently blocked off, as well.
Items
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Item
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Location
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Games
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RageCandyBar
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From the man on the east side, purchased for $300
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HG SS
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After defeating the Mahogany Gym
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TM07 (Hail)
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From Pryce upon his defeat
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HG SS
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Route 43
Route 43 links Mahogany Town to a major landmark, the Lake of Rage. Two separate paths lead to the lake; passing through the gate requires a $1000 toll paid to a pair of Team Rocket members, while the western path winds its way through tall grass and past several Trainers.
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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HG
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SS
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15, 15-17
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30%
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40%
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30%
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HG
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SS
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15
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30%
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HG
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SS
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17
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25%
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20%
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0%
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HG
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SS
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17
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0%
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0%
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20%
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HG
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SS
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15, 16
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10%
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10%
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5%
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HG
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SS
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16, 15-17
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5%
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0%
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15%
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Surfing
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HG
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SS
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5-50
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100%
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Fishing
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HG
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SS
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10
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95%
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HG
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SS
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10
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5%
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HG
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SS
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20
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60%
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HG
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SS
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20
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40%
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Headbutt
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HG
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SS
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17-18
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65%
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HG
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SS
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15-16
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50%
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HG
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SS
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15-16
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30%
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HG
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SS
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15-18
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20%
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HG
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SS
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17-18
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15%
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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
The Lake of Rage is the largest lake in the region. Heavy rains have flooded the area, causing the lake to engulf the maze-like forest to the west. These waters used to be known as a fishing spot with the liveliest Magikarp around, but now a red Gyarados dominates the entire lake.
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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Surfing
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HG
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SS
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5-20
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90%
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HG
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SS
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10-20
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10%
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Fishing
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HG
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SS
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10
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100%
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HG
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SS
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20
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97%
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HG
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SS
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20
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3%
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Headbutt
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HG
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SS
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17-19
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15%
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HG
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SS
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14-19
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20%
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HG
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SS
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14-16
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50%
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HG
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SS
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17-19
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65%
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HG
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SS
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14-16
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30%
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Special Pokémon
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HG
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SS
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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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A Red Gyarados?!
Unlike others of its species, this Gyarados evolved under mysterious circumstances which resulted in its unusual coloration.
When the battle ends, you find a Red Scale floating on the water. This can be traded to Mr. Pokémon back on Route 30 for an Exp. Share.
The Caped Crusader
When you return to shore, you meet a man in a black cape with his Dragonite. This is Lance; he has been investigating rumors that all of the Magikarp in the lake are being forced to evolve prematurely. He believes that an odd radio signal from Mahogany is the cause, so follow him back to the suspicious Souvenir Shop.
Mahogany Town
Souvenir Shop
As you enter the shop, Lance's Dragonite uses Hyper Beam to ensure cooperation from the shopkeeper. Lance confirms that the strange radio signal is coming from this location, and moves a cabinet to reveal a flight of stairs leading down into the Team Rocket HQ.
Team Rocket HQ
Trainers
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B1F
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Trainer
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Pokémon
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Guards
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Other Trainers
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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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B1F
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HG
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SS
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Trap floor
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21
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Five
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HG
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SS
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Trap floor
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23
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Six
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HG
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SS
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Trap floor
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21
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Five
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B2F
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HG
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SS
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Transmitter room
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23
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Three
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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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B1F
Each of the five Persian statues on this floor has a hidden camera that alerts the Rocket Grunts in the security center. Upon stepping in front of one, the same two Rockets show up to attack.
Take the first left and head south to the security center. Defeat Scientist Gregg, grab the Guard Spec., and examine the computer to deactivate the security cameras. Leave the room and turn east to find a Hyper Potion. Turn right and follow the south hallway. Collect the Nugget and take the stairs in the southwest.
B2F
Lance is waiting here for you, and heals your Pokémon before running off. Fight the two Rocket Grunts nearby, and take the southeast stairs to the lowest floor.
B3F
Lance informs you that shutting off the radio signal requires the voice of Petrel, one of Team Rocket's Executives. He is currently hiding out in the office to the northwest, which requires two passwords to enter. Grab the TM49 (Snatch) to the north, then battle Scientist Ross and the female Rocket in the southeast room. When defeated, she gives up the first password: SlowpokeTail. Continue on to the southwest room. Defeat the Rocket here to learn the second password, RaticateTail. Pick up the X Special and Protein near the potted plants, then head north. Grab the Full Heal in the hallway, and climb up the northeast stairs.
B2F
Examine the machinery to the south for a hidden X Sp. Def. Head west to fight another Rocket, then take the stairs back down to B3F.
B3F
Silver appears when you approach. Still reeling after being defeated by Lance, he insists that he is the one who will eliminate Team Rocket, before shoving you aside as he leaves. Take a quick detour up the south stairs to get TM46 (Thief), then input the two passwords to open the doors. Step inside to confront... Giovanni?! The real head of Team Rocket went into hiding after disbanding the group three years ago, and the copycat is Petrel, the second of the Executives. He is so confident that you will not defeat him that he reveals the password to the generator room: Hail Giovanni. Unfortunately, it only works when spoken in his voice.
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Reward: $880
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Defeated, he hurries off. After he leaves, the Murkrow that was sitting nearby demonstrates its ability to mimic voices before running off, as well. It leads you back to the generator room on B2F, then screams the password in Petrel's voice, fooling the voice-recognition system into opening the door. Murkrow leaves, and just as you enter the room, an Executive and another Rocket Grunt show up. This is Ariana, who attempts to force a 2-on-1 battle. Her plan is short-lived, as Lance shows up with his Dragonite to join the fight in a Multi Battle.
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Reward: N/A
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Reward: $2960
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Ariana claims that the experiment was a total success, and that it does not matter what happens to the hideout now. She and the other Rockets flee the town to plan their next move, and Lance goes to inspect the generator. He finds that in order to shut it down, the six Electrode that power it must be removed. He takes care of the three on the right, leaving you to battle the three on the left. With the generator disabled, Lance rewards you with HM05 (Whirlpool). Climb back upstairs and take the warp back to the entrance. With Mahogany now free of Rockets, the Gym has finally reopened.
Route 43 & Lake of Rage
Before challenging the gym, there is one more item to grab, and four more trainers to battle to gain some extra experience. Speak to the guard in the gate to get TM36 (Sludge Bomb).
Then go to Lake of Rage to battle the four trainers. After that, you should be ready to take on the Gym!
Trainers
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Trainer
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Pokémon
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After clearing Team Rocket HQ
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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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Mahogany Gym
Mahogany Town Pokémon Gym
Leader: Pryce
The Teacher of Winter's Harshness
The Mahogany Gym specializes in Ice-type Pokémon. Fire-, Fighting, Rock-, and Steel-type attacks are the most effective against Ice Pokémon, but Electric-type attacks are also effective against the Seel and Shellder families. Avoid using Grass-, Flying-, Ground, or Dragon-type Pokémon.
Pryce's Gym consists of three different rooms, and he has installed frozen tiles in each to thwart all but the most determined Trainers. Reaching him will require moving the blocks to create better stopping points.
Entrance Room
Go north to the first block, sending it skidding off to the second. Slide left, up, right, then up to the door.
Center Room
Battle Skier Dana, then walk past her and head right across the ice to the two blocks. Slide up to reach the door.
Back Room
Walk past Boarder Deandre, and slide right to the two blocks. Head up to fight Skier Jill, then slide right, down, left, up, right, up, right, then up to battle Boarder Gerardo. From here, slide left then up to reach Pryce. His Seel and Piloswine both know Hail, which calls in a hailstorm that lasts for five turns. This storm damages all but Ice Pokémon every turn, raises the accuracy of Piloswine's Blizzard to 100%, and raises its evasion due to its Snow Cloak Ability. His Seel and Dewgong can use Rest to restore health and cure status ailments, and can even attack while asleep with Snore and Sleep Talk.
Mahogany Gym
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Reward: $4080
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Defeated, Pryce awards you the Glacier Badge, which enables the use of Whirlpool in the field. He also hands over TM07 (Hail) as a prize.
The Rockets Return!
Upon leaving the Gym, Elm calls about strange radio broadcasts that mention Team Rocket. It seems that they have one more trick up their sleeve, so fly back to Goldenrod City to finally put an end to their plans.