The train comes every time in the saffron station and the goldenrod station.If isnt came is because you dont have the train pass.To get it,after you get all the badges,go to saffron city and talk to copy cat she will tell you that her clefary doll as missing.After this fly to vermillion city and go to pokemon fan club,in the table you will find her doll,talk to the guy that is close to it and he will give you the doll.Return it to copy cat and she will give you the train pass.
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train it
soulsilver and heartgold, it has the most trainers
you can ride the magnet train
trade them to heartgold
It's pretty obvious... EV train (I suggest EV Training in Defense)...