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Pokemon Gym Leaders - Violet City Gym Leader - Falkner
Falkner is Johto's first Pokemon gym leader, and he uses Pokemon of the flying-type. If you chose Chikorita as your starter Pokemon, you're in for a bit of a challenge since flying-type Pokemon trump grass-type Pokemon. Fortunately you can pick up a few Pokemon to help you along the way. On the route from New Bark Town to Cherrygrove City you'll notice a passageway to the north. This leads to Route 46, where you can capture a wild Geodude. Geodude learns the move Rock Throw at level 11, and should be sufficient to help you take down Falkner's level 9 Pidgey and level 13 Pidgeotto. Beat him to win the Zephyr Badge.
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Azalea Town Gym Leader - Bugsy
Pokemon gym leader Bugsy uses bug-type Pokemon and his roster includes a level 15 Metapod and Kakuna, as well as a level 17 Scyther. This is another instance where you'll be at a disadvantage if you chose Chikorita as your starter. Fire-type Cyndaquil, on the other hand, will perform marvelously here. You can also use rock- or flying-type Pokemon, so here's another instance where Geodude will come in handy. By this point you could have also picked up a Pidgey, Spearow, or Hoothoot. Be sure your Pokemon are at least at level 14 or 15 to win this fight. Beating Bugsy earns you the Hive Badge.
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Goldenrod City Gym Leader - Whitney
Gym leader Whitney could be your first real challenge in Pokemon Heart Gold and Soul Silver regardless of which starter you chose and which Pokemon you have on your team. Whitney uses a team of two normal-type Pokemon, a level 17 Clefairy and a level 19 Miltank. Clefairy shouldn't pose too much of a problem, but Miltank has the Milk Drink attack which restores a large percentage of its hit points. Get a Drowzee on Route 34 south of Goldenrod City for its Hypnosis attack to put Miltank to sleep, or use a Mareep from just outside Violet City to paralyze Miltank with Thunder Wave. Either way, Miltank won't be able to heal if it can't move. Whitney will hand over the Plain Badge upon defeat.
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Ecruteak City Gym Leader - Morty
Ecruteak City is home to Morty and his team of ghost-type Pokemon. Before you can challenge Morty, you'll need to find him in the Burned Tower, where he's looking for legendary Pokemon. Once he returns to his gym, prepare yourself and go back to face him. His team includes a level 21 Gastly and Haunter, level 23 haunter and level 25 Gengar. Ghost-type Pokemon are weakest to psychic-types, so you have a fair selection at this point in the game: use a Kadabra (evolved form Abra, found outside Goldenrod City), Drowzee, Natu (found in Ruins of Alph), or a Togetic (evolved from the Togepi hatched from the egg you received early in the game). Morty surrenders the Fog Badge after you win.
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Cianwood City Gym Leader - Chuck
Although you'll pass through gym leader Jasmine's home turf, Olivine City, first, you won't be able to battle her until later since she's tending to the sick Ampharos in the lighthouse. She sends you to fetch medicine from Cianwood City, where you can also battle against gym leader Chuck and his fighting-type Pokemon. Chuck has a level 29 Primeape and a level 31 Poliwrath. Primeape will crumble to the same psychic-type Pokemon you used to defeat Morty while Poliwrath can be dispensed with by a grass- or electric-type Pokemon such as Ampharos (evolved from Mareep) or Meganium (evolved from Chikorita). Beating Chuck earns you the Storm Badge.
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Olivine City Gym Leader - Jasmine
Even though you helped heal her sick Ampharos, you're still going to have to battle Jasmine to earn the Mineral Badge. Jasmine is the first gym leader in Pokemon Heart Gold and Soul Silver to use Pokemon of a non-traditional type (not featured in Pokemon Red and Blue), the steel type. Her team includes two level 30 Magnemite and a level 35 Steelix. Defeat both Magnemite with ground- or fire-type Pokemon such as Graveler (evolved from Geodude) or Typhlosion (evolved from Cyndaquil). Steelix has the same weaknesses, but can additionally be felled with water-type attacks from your Feraligatr (evolved from Totodile) or other water-type Pokemon.
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Mahogany Town Gym Leader - Pryce
Pryce resides in Mahogany Town and uses Pokemon of the ice type. His gym will be blocked off until you head north to the Lake of Rage and either defeat or capture the Red Gyrados, and then assist Lance in defeating Team Rocket in Mahogany Town. Once these conditions are met, you can do battle with this frost gym leader and his level 30 Seel, level 32 Dewgong and level 34 Piloswine. Bring along some Ice Heal, since your Pokemon are likely to be frozen solid at least once or twice. Pokemon of the fire-type, such as Typhlosion, will be strong against all three Pokemon. You can also use electric-type Pokemon such as Ampharos against Seel and Dewgong, but not Piloswine. Winning will earn you the Glacier Badge.
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Blackthorn City Gym Leader - Clair
The final Pokemon gym leader in Pokemon Heart Gold and Soul Silver, Clair, can only be challenged once you've defeated Team Rocket in Goldenrod City. Note that defeating Team Rocket earns you the Rainbow Wing in Pokemon Heart Gold or the Silver Wing in Pokemon Soul Silver, which give you the chance to capture either Ho-Oh or Lugia, respectively. Consider backtracking to capture the legendary Pokemon, as it will prove helpful in your fight against Clair. Otherwise head straight to Blackthorn City to face Clair and her dragon-type Pokemon. He formidable team consists of two level 38 Dragonair, a level 38 Gyrados, and a level 41 Kingdra. Dragon-type Pokemon are weak against ice attacks and dragon attacks. Use your Gyrados from the Lake of Rage to take out the two Dragonair and bring down Gyrados and Kingdra with an electric-type Pokemon like Ampharos. Note that you can also acquire an ice-type Pokemon such as Seel or Swinub in the ice cave north of Blackthorn City.
Clair ends up being pretty bratty for a Pokemon gym leader, and won't hand over the Rising Badge after you defeat her. Instead you'll have to head to the Dragon's Den across the pond to the north of her gym. Make your way through the cave and talk to the old man in the hut in the center, and he'll ask you a few questions about caring for Pokemon. Give answers that indicate you care for and respect your Pokemon and he'll be satisfied. Clair will show up, and after some light scolding from the old man, she'll hand over the Rising Badge.
A Pokemon Heart Gold and Soul Silver strategy guide to defeating all Pokemon gym leaders. Part 1 covers the gym leaders in Johto while part 2 covers the gym leaders in Kanto.