Instructions
Restoring Power to the Train
Talk to the manager of the Kanto Power Plant located just off of Route 9. He will tell you that a thief has stolen a crucial machine part from the plant.
Travel to Cerulean City and enter the Cerulean City gym. The thief who stole the machine part will flee to the Nugget Bridge north of town. Chase him, and then defeat him in a battle.
Return to the gym and walk onto the left side of the bridge. Face the northwest corner of the hole in the bridge. Press the "A" button to uncover the machine part and put it in your bag.
Give the machine part back to the power plant manager to restore power to the Magnet Train.
Boarding the Magnet Train
Travel to Saffron City and talk to Copycat in the house south of the Saffron City train station. She will ask you to find her lost Pokemon doll.
Fly to Vermilion City, enter the Pokemon Fan Club building and talk to the man standing next to the lost Pokemon doll. He will give it to you so you can return it to Copycat.
Fly back to Saffron City and give the lost doll back to Copycat. She will reward you with a pass for the Magnet Train.
Enter the Goldenrod City train station, and tell the conductor that you want to board the train to Saffron City.