Real life, ninja. Alchemy use for smoke bombs and poison use, some sneak attack varient. No Su or Sp abilities.
Lightly supernatural: abilities include running up vertical faces or short ranged teleportation, hide in plain sight and silent movement
Moderate supernatural: darkness manipulation, weak elemental attacks, invisibility, move silently.
High supernatural: Naruto-esq, high elemental blasting, strong Illusions, Time/space manipulation, generally spellcaster like.
I would personally build some sort of progression from the first to the latter throughout a class. Possibly with a manuver/spellcasting mechanic that slowly changes from Ex to Su/Sp abilites as you gain levels.
Final Fantasy XI had an interesting ninja class, its Ninjutsu used varying kinds of fireworks and powders for what looked like spells.