After you use the Silph Scope and find Mr. Fuji in Pokémon Tower, you should to go Saffron City to stop Team Rocket's schemes.
Explore the City
There is an X Sp. Def in the northeast corner of the city. You can get there by walking behind the Saffron City Gym sign.
Team Rocket won't let you go into the Gym right now.
In the Pokémon Center, an Ace Trainer will trade you an Alolan Raichu in exchange for a Raichu.
To the left of the Gym, there is a Fighting Dojo. Here you can talk to the Coach Trainer to battle Coach Trainer Leona, who has a level 32 Machoke and a level 33 Electabuzz. You get 3300 Pokédollars for winning. After the battle, you get TM23 Thunder Punch.
In a building to the left of the north entrance of the city, there is a girl upstairs called Copycat, whose favorite pokémon is Clefairy. If you have a Clefairy, put it in your party and take it out of its pokéball, then talk to Copycat and show her your Clefairy. Copycat will give you TM08 Substitute.
Check near the top of Copycat's bed to find a hidden Moon Stone.
In a house east of the Pokémon Center, you will find Mr. Psychic. He will give you TM40 Psychic when you talk to him.
You can battle the trainers in the Fighting Dojo. North of the Ace Trainer, you can battle Black Belt Hitoshi, who has a level 31 Primeape. You get 868 Pokédollarsa and 3 Poké Balls for winning.
Across from Hitoshi on the left side of the room, you can battle Black Belt Aaron, who has a level 31 Graveler. You get 868 Pokédollars and 3 Poké Balls for winning.
North of Hitoshi, on the right side of the room, you can battle Black Belt Hideki, who has a level 31 Poliwhirl. You get 868 Pokédollars and 3 Poké Balls for winning.
Across from Hideki, on the left side of the room, you can battle Black Belt Mike, who has a level 31 Machoke. You get 868 Pokédollars and 3 Poké Balls for winning.
At the top of the room, you can fight the leader, Karate Master Koichi, who has a level 34 Poliwrath. You get 952 Pokédollars for winning. After the battle, you can choose to take Hitmonlee or Hitmonchan (you can only choose one). Hitmonlee has a higher base Attack and Speed, while Hitmonchan has a higher base Defense.
In the center of the city, walk toward Jessie and James to see a cutscene. Afterward, go into the Silph Co. building.