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.
The Lake of Rage is the largest lake in the region, and exists alongside a maze-like forest to the west. The area is known for its Gyarados population, and the most notorious resident is visible just offshore. Bring a decent Poké Ball supply and swim out to meet the 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.
Climb back onto shore and speak to the man reading the sign. 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-looking shop.
Upon entering 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 stairway leading down into the Team Rocket HQ.
Take the first left and head south to the security center. Defeat Scientist Jed, 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 walk along the south hallway. Collect the Nugget and go down the stairs in the southwest.
Rocket Hideout, B2F
Lance is waiting for you here, and heals your Pokémon before running off. Beat up the two Rocket Grunts nearby, and take the southeast stairs to the lowest floor.
Rocket Hideout, B3F
Lance informs you that two passwords are required to reach the boss. Grab the Full Heal to the north, then battle the Scientist 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 the Protein by the potted plants, then head north. Grab the Ice Heal in the hallway, and climb up the northeast stairs.
Head south to pick up a hidden Full Heal next to the computer, then head all the way to the west, where you are challenged by another Rocket. Go down the stairs to reach the boss's room.
Take a quick detour up the south stairs to get TM46 (Thief), then head towards the doors. When you approach them, your rival appears and insists that he is the one who will eliminate Team Rocket. After he leaves, pick up the Ultra Ball at the end of the hall, then input the two passwords at the door to enter the boss's office. The Executive here talks about Giovanni disbanding the group three years ago, and how the organization has continued on since then, planning for his return.
Defeated, he runs off to warn the others that their plans are in trouble. Talk to the Murkrow in the corner to learn the password for the generator room, Hail Giovanni.
After entering the password, an Executive and a Grunt ambush you in an attempt to force a 2-on-1 battle, but their plan is short-lived. Lance shows up with his Dragonite, and the two of you each battle a single Rocket.
They claim their experiment is a success, regardless of their defeat here. Lance inspects the generator, and claims that in order to shut it down, the six Electrode powering it must be removed. Catch or defeat the three on the left to put an end to Team Rocket's plan. With the machine disabled, Lance rewards you with HM06 (Whirlpool). Follow him upstairs, grab the hidden Revive, and take the warp tile back to the entrance.
With the town now free of Rockets, the Gym has finally reopened.
MAHOGANY TOWN POKéMON GYM LEADER: PRYCE
The Teacher of Winter's Harshness
The Mahogany Gym specializes in Ice-type Pokémon, and Pryce has installed frozen tiles to thwart all but the most determined Trainers. The most direct route to the Gym Leader can be made in six moves. Stand by the Poké Ball statue on the left, and slide up twice to the first Boarder. Slide right, down, left, up, and right again to meet Pryce. 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 bringing Grass-, Flying-, or Ground-type Pokémon.
Upon leaving the Gym, Elm calls about strange radio broadcasts that mention Team Rocket. It seems that the gang has one more trick up their sleeve, so fly back to Goldenrod City to finally put an end to their plans.