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* The finding of New Hyrule by Link and Tetra. How in the world could an entire continent of landmass just not be known by anyone, but then suddenly appear, with sailing being the one and only means of travel by the world's survivors for generations in hundreds of years? Simple: it wasn't ''there'' yet. The entirety of Hyrule had a barrier keeping the waters out, stretching so high as to be at what would have been sky level. When the King of Hyrule finally saw it destroyed, the waters would have ''greatly'' receded, by potentially up to thousands of feet. It isn't that New Hyrule had somehow been missed, it only emerged ''after'' the old Hyrule was mercifully destroyed.
* The Sand 'Realm' is, technically, in the Ocean Realm. Spirit Tracks is a rough sequel to Wind Waker and Phantom Hourglass-- the latter of which placed an emphasis on sand... in an ocean setting. It's also been noted, elsewhere on this wiki, that the Ocean Realm's symbol resembles an hourglass. Might be a coincidence, might be an obscure ContinuityNod / MythologyGag (hard to tell which with the continuity, sometimes.)
* The colors on the pipes of the Spirit Flute all correspond the six Lokomos you meet: [[spoiler:Gage, Steem, Carben, Embrose, Rael, and Anjean.]]
* While playing the Snow Temple, you'll notice that the completed bell puzzle sounds exactly like the first bit of "Do You Hear What I Hear." Snow Temple... snow... winter... Christmas...
* This incarnation of Zelda is noticeably feisty, even if she tries to play the princess' part dictated "by family tradition". Why? She's Tetra's granddaughter. She must have inherited some of the pirate genes.
* Why Fraaz needs to inflate to use his fire-based abilities:
** Snow often falls at higher elevations, and the air gets thinner the higher in elevation you go so he would need to be able to take in large amounts of air to fuel his magic.
** Alternatively, due to less air pressure by elevation, he's sucking in the same air he needs, but the air can expand more, due to less air pushing back, thus making him bigger than he would normally need to.
* Link receiving the Shield of Antiquity from Niko becomes this when you consider that the shield the Hero of Winds used in ''The Wind Waker'' (which was also identical to the one used in ''The Minish Cap'') was said to be a family heirloom. Maybe he wanted continue that tradition by leaving a similar memento for Niko or to bequeath to one of his descendants, if he had any. (Though it's still a mystery why he would choose to leave the less-significant shield from ''Phantom Hourglass'' as opposed to one of the ones from ''The Wind Waker'', the latter of which also included said heirloom.)
On the [[Headscratchers/TheLegendOfZeldaSpiritTracks headscratchers]] page.