I have a lvl 10 Ninja with the template Missing (so a total lvl of 13). Considering that the template allows the Ninja to become invisible, that means that Magic Missile would be ineffective because I have total concealment.
However, if I was stealthing & the person I was fighting casts True Seeing, would Magic Missile work regardless of how well I'm stealthed? (my overall stealth w/o d20 is 72)
My theory is that Magic Missile is like a Line effect (goes only in a straight line) and therefore must be aimed in the general vicinity of where I'm located. If my reasoning if false, then my opponent can cast Magic Missile in the complete opposite direction of where I'm located & still hit me.
The missile strikes unerringly, even if the target is in melee combat, so long as it has less than total cover or total concealment.
If you (the target) fufil those conditions (not having total concealment or total cover) at the time of casting, it hits you.
True seeing negates invisibility. Your stealth score doesn't matter if the mage knows where you are. If your stealth was good enough, the mage wouldn't see you to be able to target you (invisibility nothwithstanding).
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Magic missile is not a line in the AoE sense. It will automatically hit any target the caster can see. If the caster can see the Stealthy Ninja after casting True Seeing (that is, his Perception roll is better than the Ninja's Stealth check less the modifiers for invisibility), then the Magic Missile will hit the target. If not, then he does not see the ninja and cannot therefore target him.
EDIT: Ninja'd ... dang stelathy ninjas! <casts magic missile>