The Magnet Train Pass allows you to travel back and forth between the Kanto and Johto regions without any limitations. The Magnet Train is really just a way to travel between the two regions at any time without using Fly twice or having to wait until certain days.
There is no exact answer as to what you should do after you get the Magnet Train Pass. Really, you are free to do whatever you want. Some ideas would be to battle Red on Mt. Silver, collect all the gym badges if you haven't already, challenge the Battle Frontier, complete the National Pokedex, or challenge the gym leaders to rematches. There are no limits to what you can do after you have obtained the Magnet Train Pass and have completed the main storyline for Johto.
after you get the magnet train pass use the magnet train
go to magnet train manger and ask him to give you a train pass
you can ride the magnet train
You can use it to take the magnet train to kanto I think.
there is a pink house at saffron city and there is a girl inside it you have to find her clefairy doll and she wiil give you a magnet train pass.
you have to find copycats clefairy doll give it to her and she will give you a magnet train pass hoped it helped you out kieran Thompson
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Get on the magnet train and it will take you to Goldenrod city. You can back and forth between johto and kanto easily using the magnet train, but it's not essential.
You can now use the train from kanto to johto.
You talk to the copycat girl in the city with the magnet train in Johto and bring her her pokedoll from viridian in Kanto
you go to the Pokemon tower
She gives you a magnet train pass.