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Darkness, often also referred to as Shadow, is a pivotal element that has played a vital role in The Legend of Zelda franchise. It has served various purposes, both storyline-wise and gameplay-wise, and usually as a manifestation of evil (but not always).
Role in the Series
Darkness as a symbolic element
Of all the elemental staples in the series, such as fire, ice or light, darkness has carried over the worst reputation. The reason for this is because this is the signature source of evil in the World of The Legend of Zelda and, most importantly, it is even the origin of the evil beings and creatures that overrun the Light World. Though the line between what is good and what is evil is not always clear, it is known that there has always been a contrast between light and dark, with Link striving in favor of the former. As detailed below, darkness is frequently portrayed through a setting that is more difficult to conquer than the Light World. In some games, Link himself is occasionally forced to fight his dark counterpart as well.
That said, darkness does not always symbolize evil. In Ocarina of Time, aside from the portrayal originated from Ganon and his servants, darkness is canonically represented in the same way the other elements are. That representation, the Shadow Temple, offers several puzzles, obstacles and enemies revolving around it, and is guarded by the Sage of Shadow (by the moment the events of the game take place, Impa fulfills that role, and also guards the Shadow Medallion until she gives it to Link). The Nocturne of Shadow pays homage to the element as well, and instantly transports anyone playing it to the backside of Kakariko Village Graveyard, where the temple is located.
Darkness has been represented by several benign races over the course of the series. One of them is the Sheikah, a near-extinct race who used to protect the land of Hyrule secretly; the Ikana Kingdom, no longer belonging to the world of mortals, overruns a major region of Termina when the Skull Kid invades the Stone Tower Temple in Majora's Mask; the Twili, formerly the Interlopers in Hyrule, was a peaceful race inhabiting the Twilight Realm until Zant's rise to power; etc.
Darkness as a setting
In addition to the shadow dungeons located through Hyrule and several other lands, there are also entire overworld locations that revolve around housing the creatures of darkness. The Dark World, in A Link to the Past, is a notable example, as every location from the Light World has a geographically direct counterpart in the other setting, which also shows a more evil vibe (for example, Village of Outcasts when compared to Kakariko Village). This applies, to a lesser extent, to the landmarks of Hyrule in Twilight Princess when covered by the influence of Twilight by Zant and the de-powering of the Light Spirits who guard the different provinces.
In most cases, when Link stands on a place cursed by a dark force, he is affected in one or another way; in the aforementioned examples, the side effect is shapeshifting. Dark Fog, also located on dark places, affect the young hero the same way. In the Temple of the Ocean King, Link loses Sand of Hours continuously when he is not within a safe zone. There may be a higher population of enemies (and some of them being undead) in these places as well.
Darkness as a puzzle device
In some Stealth missions, such as the infiltration in Deku Palace (Majora's Mask) or in Forsaken Fortress (The Wind Waker), it is convenient to remain in the darkness, and some hunt-based sidequests are best taken place at night. Likewise, in Spirit Tracks, some dark rooms house bombable walls that remain unnoticeable if there are lit candles, and Dark Ore must be transported under as little sunlight as possible.
To date, there has been only one dark weapon usable by Link as an item. This item is the Fierce Deity's Mask, so far exclusive of Majora's Mask, which allows the wearer to turn into Fierce Deity Link and become capable of performing unmatched devastating attacks, enough to defeat bosses very quickly. It is hinted that the powers of this mask are as evil as those of Majora's Mask itself, but it can only be used during boss battles without glitches.
In the particular case of Twilight Princess, Midna allows Link to make use of dark powers, although only as long as Link is within his wolf form. One of these abilities is creating a field of energy that surrounds enemies, and allows the young hero to attack them all almost instantly. In wolf form, Link can also activate senses that allow him to see otherwise invisible objects, spirits, and scents (but his sight is darkened significantly). Also, Midna can teleport both Link and any big and heavy object from one landmark to another. Finally, when Midna is in possession of the entirety of the Fused Shadow, she is able to transform into a spider-looking entity with deadly powers. Because she is the only one capable of using such dark powers without being corrupted by them, they aim to retrieve both the fragments of the Fused Shadow and the fragments of the Mirror of Twilight, as regular enemies and characters otherwise mutate heavily into evil, dangerous monsters due to them.