The Prison Bottle is a special item that can be used on Hoopa to change its form from Hoopa-Confined to Hoopa-Unbound for three days. After three days, it will revert to its Confined form. Storing Hoopa in the PC will also revert it.
Note: Hoopa is currently bugged: once changed to its Unbound form, it can't revert at all. This should be fixed soon.
A Prison Bottle is held by every wild Hoopa, thus one is obtained when any Hoopa is captured.