- Why is it that even though it was stated that the properties of the Dark World cause those who enter it to shapeshift into something that reflects their true natures, Agahnim looked exactly the same as he did in the normal world? Agahnim is basically nothing more than a host for Ganon's spirit; he has no soul of his own, and Ganon was already changed into his boar form.
- The three pendants you have to collect (Courage, Strength, and Wisdom, respectively) seem to have no reason for the order you gathered them in, but now they seem to be in order based on how soon Link (and by extension, the player) would gain those respective traits. Courage comes first because you need it just to start your journey. Strength follows after you have started gaining new items and powers. Wisdom comes last since Link and the player need time to master these items and become comfortable with the gameplay.
- Each of the dungeons Link has to beat to get to the pendants: The first dungeon is straightforward and easy as long as you have the courage to take action, the second is just one big monster pit that you have to fight through as a test of strength and the final dungeon is a big puzzle that you must be wise enough to solve. Even the bosses reflect these virtues: the Knights die quickly and easily as long as you take action, the worms are a matter of doing more damage to them than they can do to you and the final boss is a puzzle where you have to figure out where to hit while not getting knocked out of the arena.
- The Master Sword was specifically forged as a failsafe in case the Triforce was used for evil. The Master Sword suppresses the Triforce's power, making the holder of the Triforce powerless. Still some Fridge Brilliance here: Ganon wasn't hosting the Triforce in his body at the time — it was in a locked room behind his chamber in the Pyramid. The Master Sword was still a sword, so it could be used for the first half. After that, Ganon used his magic to make himself invulnerable, which only Silver Arrows could undo.
- The Ice Rod is inherently fatal to the Sand Worms because the desert is a very dry and hot place. Technically speaking, frozen moisture is the antithesis of sun-baked sand. Much like the Fire Rod is inherently fatal to Kholdstare.
On the headscratchers page.