To get the master ball you need to do a series of things, start by doing the following:
Get through Rock Tunnel which requires you to know the FLASH and CUT HMs. Go straight to Celadon city. Visit the Celadon Mansion, there should be a guy next to it facing away from you. When you talk to him he will say, the nice lady in Celadon Mansion gave him tea but he burned his tongue with it. Now go inside the Mansion and have the rich lady give you the tea. With that tea you can open the way to Saffron City later on. If you find a way to go through the back door of the mansion, you can find an Eevee inside an item ball, on top of a table!
Now go to one of the buildings south of the Game Corner. One of them is a restaurant, in which the man sitting on the table will give you the Coin Case.
Next to that restaurant there is another building where there are a couple of Rockets. One of them will tell you that there is a basement under the Game Corner, another will tell you that there is no such thing as a switch behind the poster.
Now head to the Game Corner, battle the Rocket guarding the poster. If he does not want to battle you, but instead he tells you to buzz-off then you need to beat the gym in Celadon first. Go out and Cut the bush in front to get in, after you beat the gym go back to the Game Corner.
After you battle the Rocket guarding the poster, you need to work your way through a very tough maze, your objective is to get the key to the elevator. In this place, you will get something called a Silph Cope. It will allow you to go to the Pokemon Tower in Lavender Town. Ghosts in the tower will become visible with the scope.
When you reach the top of the Pokemon Tower a Marowak will attack you. Best to let this Marowak go (faint it) because it is required to beat the game. On that floor Mr. Fuji will thank you for letting Cubones mother rest. He will reward you with Poke Flute. BTW if you want your own Marowak, catch a Cubone and it will evolve to a Marowak.
Once you have the Poke Flute, now you can go to Saffron City. Go to the biggest building which is called Silph Co. The flute is not directly needed to enter Saffron, but if you come before getting the Poke Flute; the Rocket at the door in Silph Co. wont let you in.
Again the battle with the Rockets here is brutal, and this place is twice as big as the Game Corner. After you have beaten Giovanni, the president of Silph Co. will reward you with a master ball.