So what you basically mean is that the item has both good and bad effects on the story/character, right? If so, here's some suggestions -
1.Get the item required to catch a certain legendary pokemon, and when you use it, the pokemon will cause chaos and destroy PCs (or maybe not) and you'll no longer be able to heal your pokes. (for a limited time of course)
2.Get a Fire/Water/Grass/Any other type ID card which boosts all stats of the pokemon of the corresponding type, but you won't be able to use pokemon of any type other than the card's.
3.Get a potion that never ends (or gets refilled after a certain amount of time), at the cost of never being able to buy any other healing item again.
Well, these items were of course a bit too much, EXTREMELY TOO MUCH. If I get a rough idea of the storyline, or maybe the character, then I could share some other ideas too.