Hi! Saffron City is a big city with lots of buildings.
It has four entrances: Cerulean City, Lavender Town, Vermillion City, and Celadon City. Remember, you had to take the underground paths because some buildings would not let you through? Give one of these guards a drink from the vending machine in Celadon PokeMart and they will let you through.
Saffron City has the famous Silph Company, which is now being ruled by Team Rocket, Fighting Spirit Dojo Gym (not official), Sabrina's Gym, Pokecenter, Pokemart, and houses. The Pokemart offers the Hyper Potion, an item that heals your HP by 100.
The Fighting Dojo is not an official gym; you will not get a badge. But you will get a pokemon if you beat it. This gym has the Blackbelt and four of his trainers. They all use fighting pokemon. Use flying and psychic typed pokemon to beat them. I advise you to use flying attacks such as Fly and Wing attack, and psychic attacks such as Psychic and Psybeam to kill them. This minor gym is very easy.
The leader, Blackbelt, uses only two fighting pokemon: Hitmonchan the Punchy Pokemon, and Hitmonlee the Kicking Fiend. Both are at level 37. Watch out for Hitmonchan's Comet Punch and Ice Punch.
When you beat Blackbelt, he will give you one of two fighting pokemon: Hitmonchan or Hitmonlee. Hitmonchan can have attacks such as Comet Punch, Mega Punch, Ice Punch, Fire Punch, and Thunder Punch but it's special is very low so the last three punch attacks would not hit that much damage. Personally, I would choose Hitmonlee.
Silph Company is the large and tall building beside the Pokecenter. There is a Team Rocket member guarding the door. Have your Pokeflute with you. If you have your Pokeflute with you, the guard will step aside and fall asleep. There are in total fifteen floors in this building. You can take the stairs or the elevator. The elevator does not go to every floor though. The elevator only goes to the floors 1 through 10, I think. There are warp tiles that will teleport you to another tile. There are lots and lots of tiles in the building. Do not go into any of the tiles yet. There are some doors that are locked. You can get the Card Key to open them later. For now, just beat the Team Rocket trainers through floors 1 to 9.
On the ninth floor, go in the tile located near the table in the bottom right corner.
When you are teleported, immediately go down and then right through the little path. In the middle is a pokeball containing the card key. To open doors with the card key, simply face the door and press A.
Now that you have the Card Key, go back to the second floor and open the doors so you can get the pokeballs and fight the trainers too. You can now go to the tiles and fight the other Team Rocket trainers. When you have beaten all the trainers, go back to the ninth floor. Open the doors on the left with the Card Key. Go to the tiles.
You will finally come to a small room with two people: Gary and another person. This is the last time you fight Gary before you beat him at the Elite Four. I assume he will start with a Pidgeot. Use a Pikachu first. He should also have a Kadabra. His last pokemon will be his starting pokemon. His levels, I think, are in the high thirty's. When you beat Gary, talk to the other person. He will thank you for your efforts and give you Lapras, the water transport pokemon at level 15.
Go through the other tile to the final floor with Giovanni. Fight the trainer there. Open the door with the Card Key. You may want to go to the computer first to switch pokemon. Beat all his trainers before fighting him, because once Giovanni is beaten, you can't fight his trainers anymore. I remember that Giovanni likes to use rock and poison pokemon. He should have a Nidorino, Nidorina, Ryhorn, and maybe Rhydon. Use water and psychic pokemon to beat him. He is pretty easy to beat. When you beat him, talk to the Silph Company president. He will give you a Master ball as your reward. The Master Ball is the most upgraded pokeball. It has a 100 percent capture chance. Use this ball to capture Mewtwo at the very end. You can use the Master ball cheat to have more but you still need one to start the cheat. Now that you have beaten Team Rocket, the members will flee town. The many houses which were blocked by Team Rocket are free again.
Go to all the houses. One is Mr. Psychic's house, who will give you TM 29, Psychic. There is one house with two floors. On the first floor are two adults. Go up the stairs and you will see their daughter, who loves to mimic people. Give her a Pokedoll and she will give you TM 31, Mimic.
Now you can fight Sabrina and her trainers. Sabrina and her trainers all use psychic pokemon. However, her gym contains small rooms that all have four warp tiles in every one. Fight all her trainers first. Then follow the path marked with numbers in the map above. Use bug pokemon to fight them. You could also use normal pokemon with strong normal typed attacks because some psychic pokemon have low defense. Do not use grass or poison typed pokemon to fight them.
Sabrina uses four psychic pokemon: Kadabra level 38, Mr. Mime level 37, Venomoth level 38, and Alakazam level 43. Use normal attacks to fight her Kadabra and Alakazam. This gym could be a little difficult.
When you beat Sabrina, she will give you the Marsh Badge and TM 46, Psywave. The Marsh Badge allows all pokemon up to level 70 to obey you.