After you defeat the Team Rocket Boss and get the Silph Scope, you can return to Pokémon Tower and reveal the ghosts within.
Climb the Tower
Go up the stairs until there is a cutscene. You will use the Silph Scope to reveal the ghosts. (If you don't have the Silph Scope, you should exit the tower and go to Route 8 for now.) After you use the Silph Scope, wild pokémon can randomly appear in the tower, including Zubat, Gastly, Haunter, and others.
Go north and you can battle Channeler Hope, who has a level 25 Gastly. You get 1000 Pokédollars and 3 Poké Balls for winning.
To the right of the Channeler, there is an Awakening.
East of that, there is a hidden Star Piece.
Go west, then south past the stairs, then east. You can battle Channeler Patricia, who has two level 25 Gastlys. You get 1000 Pokédollars and 3 Poké Balls for winning.
Go north and you can battle Channeler Carly, who has a level 25 Gastly. You get 1000 Pokédollars and 3 Poké Balls for winning.
Near Carly, there is a Super Potion.
Go east and up the stairs.
Go west to find an Escape Rope.
Go farther west to find TM04 Teleport.
Go northeast and look behind a grave to find a Full Heal.
West of that, you can battle Channeler Laurel, who has a level 25 Haunter. You get 1000 Pokédollars and 3 Poké Balls for winning.
Go north from the Channeler, then east, and check the ground to find a hidden Super Potion.
Go south, then east, and you can battle Channeler Jody, who has a level 25 Gastly and a level 25 Haunter. You get 1000 Pokédollars and 3 Poké Balls for winning.
In the southwest part of the room, you can battle Channeler Paula, who has two level 25 Gastlys. You get 1000 Pokédollars and 3 Poké Balls for winning.
Go to the west side of the room and go up the stairs.
Go northeast and you battle Channeler Ruth, who has a level 25 Haunter. You get 1000 Pokédollars and 3 Poké Balls for winning.
Go north, then west, to get a Nugget.
Step on the glowing blue symbol in the middle of the room to heal up your pokémon.
Go southwest from the symbol and you can battle Channeler Karina, who has a level 25 Haunter and a level 25 Gastly. You get 1000 Pokédollars and 3 Poké Balls for winning.
Go east and you can battle Channeler Janae, who has four level 25 Gastlys. You get 1000 Pokédollars and 3 Poké Balls for winning.
Go west from there to get an Ice Stone.
Go east from there and search the ground south of the graves to find a hidden Big Pearl.
Go north, past the stairs, and you can battle Channeler Tammy, who has a level 25 Haunter, and two level 25 Gastlys. You get 1000 Pokédollars and 3 Poké Balls for winning.
Heal up at the protective circle, then go east and up the stairs.
At the top of the stairs, you can battle Channeler Emilia, who has three level 32 Haunters. You get 1280 Pokédollars and 3 Poké Balls for winning.
Go south and you can battle Channeler Angelica, who has two level 25 Gastlys, and a level 25 Haunter. You get 1000 Pokédollars and 3 Poké Balls for winning.
To the right of Angelica, there is a Revive.
Go north past the stairs and you will battle Channeler Jennifer, who has a level 25 Haunter. You get 1000 Pokédollars and 3 Poké Balls for winning.
To the right of Jennifer, there is a set of 3 Ultra Balls.
Go west and you will find a Hyper Potion.
Go south and there will be a cutscene.
If you arrived here without the Silph Scope, you will have to leave the tower and go to Route 8 for now.
If you have the Silph Scope, you can go west and check behind a grave to find a hidden PP Up.
Then go south to find a Rare Candy.
Then go to the right and go up the stairs.
Go north and there will be a cutscene. After that, go north and there will be another cutscene. You will battle Team Rocket Jessie and James. You will have a double battle vs. their level 34 Weezing and level 34 Arbok. You get 3264 Pokédollars for winning.
After the battle, talk to Mr. Fuji. You'll automatically go to his house, and he will give you the Poké Flute.
Now that you have the Poké Flute, you can use it to wake up the sleeping Snorlaxes in Route 12 and Route 16. When you wake it up, you have to battle it, and you have to defeat it within five minutes. After you defeat it, you can try to catch it. Each one is a level 34 Snorlax.
When you are ready, go toward Saffron City. When you reach the gatehouse and try to pass or try to talk to the gate guard, he will take the Tea that Brock gave you. He will also share it with the other gate guards, so now you will be able to reach Saffron City from any of the surrounding gatehouses.