Instructions
Go to Cerulean City in the northeast of the Kanto region, and head out of town east on Route Nine. Use a Pokemon's "Surf" move to go south on Route 10 until you reach the Power Plant.
Head inside the Power Plant and talk to the man inside. He will tell you that someone has stolen a Machine Part.
Go back to Cerulean City and go to the Pokemon Gym. As soon as you enter, a member of Team Rocket will run out. Go to the top left corner of the swimming pool in the Gym and press "A" to find the missing Machine Part.
Head back to the Power Plant and hand in the Machine Part to restore power to the Magnet Train.
Go to Saffron City in the east of Kanto and head to the Copycat's House in the northwest of the city. Speak to Copycat inside and she will tell you about her missing Poke Doll.
Go south to Vermillion City and go into the Pokemon Fan Club directly to the north of the Pokemon Gym on the west side of town. Talk to the man inside to get the missing Poke Doll.
Head back to Saffron City and give the Poke Doll to Copycat in her house to get the Magnet Pass. This allows you to ride the Magnet Train between Johto and Kanto whenever you like.