You still have to see it outside of Mt. mortar in route 42, then it goes to vermillion city in kanto where you will see it again. then it will be in route 14 in kanto, then finally it will be in route 25 by bill's house after beating misty.
PS: if you accidentally make it faint, it will reappear at the burnt tower, you will have to defeat the elite 4 again though.