no where he stays there and you can go battle him again any time you want to level your Pokemon 2 100
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He disappears until you beat the Pokemon league again.
first go to the red paint then you go to the ears and then you go to the red tool thing and go from there.
go on to red tube
beat red and go to silph co.
Red will disappear to a place in which you cannot find him however if you beat Lance again then Red will re-appear back on the top of Mt. Silver and he will have the same identical party.