on rightclick with empty bottle:
name of player's tool = "Ninja"
apply invisibility to player for 5 seconds
on rightclick with redstone:
name of player's tool = "Iron"
set {god::%player%} to now
on damage:
{god::%victim%} is set
time since {god::%victim%} > 5 seconds:
delete {god::%victim%}
stop
cancel event
on quit:
{god::%player%} is set
delete {god::%player%}
Nie napisałeś tego, ale domyślam się, że pewnie chcesz graczu zabrać ten item, dlatego po linijce 6 oraz 3 musisz wtedy dodać:
set player's tool to (item amount of player's tool - 1) of player's tool