"I believe in Christianity as I believe that the sun has risen: not only because I see it, but because by it I see everything else."
~ C.S. Lewis
C.S. Lewis was ahead of his time in much of his thinking. He saw the world in such a way that would allow him to consider God's hand in everything from the good and the bad. While not everything that happens in life is good, it works together for good. The beauty about fantasy whether it's from the pages of a book or the game console is that a lot of things are up for interpretation. The way we see things comes right down to the way our souls interact with our creator. Some people have chosen to live their lives away from God and see things through the scope of their own desires. For a believer, even something as simple as a video game can hold a Godly message. For me, the Legend of Zelda is one of those games.
Recently, Nintendo released the official Legend of Zelda Timeline. While this threw the fans into an uproar, especially those who identified as "linear timeline theorists", it gave us some perspective on not only how the games relate but how Hyrule's history is influenced by the power of choice.
Firstly, let's look at the founding of the world. The Zelda universe starts out with The Legend of Zelda: Skyward Sword. It opens with a short story of the lore of the events that came before the start of the game. Strangely enough, there is no mention of the three golden goddess' of Hyrule that, in later games, are said to have been the creating force behind the world. Instead we are introduced to Hylia, a goddess who held an "ultimate power" passed down by the gods (not goddesses) of old. There's no number given to the gods, no names, and they are identified as males rather than female. (This is interesting if you know Zelda lore.) She is soon met with hoards of dark beings that rose out of the earth to begin a massacre of all those that lived on the surface. Hylia sent the "ultimate power" into the sky along with a small population of people on board a large chunk of earth to protect both the power and the people that would guard it. She and those who remained managed to seal the evil but as the game goes on you discover this seal is hardly enough to contain the darkness.
One thing I find fascinating is that while she is supposed to be a goddess, Hylia is strangely vulnerable. She is charged with protecting this power but she sends it away instead. She is also made mortal later on and takes Zelda as her vessel. While she's said to be a goddess, Hylia is shown to be very vulnerable and mortal. On multiple occasions Link has to save her from Demise, the villain of the game.The goddesses of Hyrule are mentioned, but not as goddesses. They're mentioned only when you learn songs to open up certain locations within the game. "Din's power", "Nayru's wisom", and "Farore's courage". In the games, the goddess' are shown as actually very vulnerable, even when they do arrive in later games. In the Oracle games, you actually have to save Din and Nayru. The goddess' in Hyrule's lore are shown to be not only incapable of demonstrating the power credited to them in Ocarina of Time, but unable to defend themselves from mortals themselves. Spells and songs are attributed to them, but they don't bestow these things personally. These things are given to you through another party, namely the great fairies or Fi in the case of Skyward Sword.
In all three timelines, belief in these goddess' seems to wane to almost nothing. In the fallen Hero Timeline, which is the one I find to be the most compelling for a Christian Message, Link actually takes up a shield bearing the Christian Cross on it towards the end of the timeline. In A Link to the Past, the original context for the "Book of magic" and the"Sanctuary" was "The Bible" and "Church". The Bible item even has a Christian Cross on the cover. Even official artwork from the original manual of the game shows Link praying in front of a crucifix. Even in the other timelines, mention of the three goddesses is minimal and there seems to be an abandonment of the old beliefs of Hyrule.
Let me back up a bit.
In Ocarina of Time you learn the creation mythos of that time period. There's no mention of the goddes Hylia, that's simply the name of the world now. You hear about the three goddess' that are credited with the creation of Hyrule itself- Din who represents fire and power, Nayru who represents water and wisdom, and Farore who represents the earth and courage. The goddess' are also credited with creating the Triforce, the "Ultimate power" mentioned in Skyward sword with the power to grant the wish of anyone that holds it. The Triforce is a golden relic that splits into three when one piece is touched and seeks out spirits who bear the strongest spirits representing the pieces- power, courage, and wisdom. When all three bearers are brought together and the pieces are combined once more, a wish is granted. This mythos is a little odd seeing as it was gods who were credited with creating the Triforce, not goddesses. It's also odd that the goddesses are depicted and spoken of as being golden.
One interesting fact is that the names of the goddesses are a part of three elemental dragons that protect certain areas of Hyrule. Eldin for Din, Faron for Farore, and Lanayru for Nayru. Only one of these dragons is said to be female (just an intersting side note) and none of these dragons are truely godly. In fact, you have to save the lives of two of them. It's possible that the goddess' find their origin within the dragons of ancient Hyrule and became icons as time went on.
Parallels to this are the three parts of the Holy Trinity: God the father, God the Son, and God the holy spirit. Three parts to one whole. The parts of the triforce have heavy reflections in Christianity as well. In reading on the gifts often given to those who receive the holy spirit, three stand out especially: Power, courage, and wisdom. Samson, for example, was given great power beyond that of a mortal man when the Holy Spirit was laid upon him. Soloman was said to be the wisest man to ever live and he too was gifted by the Holy Spirit. The Holy Spirit was with David when he fought Goliath granting him great courage through his faith. Time and time again these three traits are seen given to those who the Holy Spirit falls onto.
When we get to OOT, the world has embraced the idea of three golden goddesses, much the way the Israelite people embraced the golden calf and worshiped them rather than the true God. In OOT there are three timeline splits, and I theorize each of these splits represents the wishes of each of the three bearers of the triforce. In one, Link is killed, fulfilling Ganon's wishes. In one, Link slays Ganon and saves Hyrule which was his goal. Afterwards he is sent back to the past so he can live his childhood out. This is known as the Child timeline. The third Link still saves Hyrule, but he's sent away to live his childhood at Zelda's request. Unfortunately, when Evil returns there is no hero to stand in its way.
In the fallen timeline, it seems that the people of Hyrule lose their admiration for the three goddesses. In the very next game there is no mention of them anywhere. Instead of temples of the goddesses there are Churches. Instead of stories of origin, there are Bibles. Following Link to the Past comes the Oracle games where the distrust in the divinity of the goddess' is only confirmed. When Link rides to check on the Trifore, ensuring its safe keeping, he finds himself taken to alternate realities where he must save two of the goddess' of his world's old religion. They were easily tricked, easily captured, and easily put into harm's way. It took Link, a mortal, to save them and restore order. Armed with only his courage and a sword- he managed to take down a threat that the supposed goddess' were unable to even predict.
On his way back from these other worlds, Link is shipwrecked and forced to awaken yet another deity to get him on his way home. Unfortunately at the end of the game he finds that this deity was really a dream or a vision rather than a real being. I find this game to reflect the story of Jonah quite well. Link is sailing for an unknown reason, perhaps to flee from his responsibilities to tell Hyrule about the falsehood of their own religion, and meets with a storm that swallows him up. The 'god' of the world he 'wakes' in is a massive whale that he must awaken. When the game ends, Link is seen on a piece of driftwood watching the island vanish. It could be that this is his "Belly of the Whale" experience, forcing him to realize the reality of Hyrule and its lore.
Upon his return to Hyrule, we see Link in the next two games taking up the shield bearing the Christian cross, praying at the alter, and rising up against Ganon once more.
In the child timeline, Hyrule falls into shadow and the goddess seem to have become forgotten. Instead, their names are spoken of only through the names of the Light Spirits that, strangely, bear the same names as the dragons from Skyward sword. In this game, the spirits take beast forms. Like the goddess, and the dragons, they find themselves weakened by the evil within the world and are in need of Link's rescue.
In the adult timeline, Noah's flood is reflected in the worldwide flood that covers the land of Hyrule following Link's disappearance and Ganon's return. This reflects pretty well on the Noah story as God flooded the world itself to wash away the over-whealming evil that was spread across the surface of the world. In this game, the goddess are mentioned only through the three pearls that you have to collect. There is a tower of the gods, but there's very little actual reverence of the old religion of Hyrule. Instead it seems the world is moving away from the gods entirely. In spirit tracks the only force for good from the supernatural that is identified are the "spirits of good" which supposedly sealed up the evil that plagued New Hyrule.
So of all the three timelines, the fallen hero timeline moves the world towards what seems to be a Great Awakening of sorts. While the religious references were removed by Nintendo of America for political reasons, they're still part of the games themselves. It reflects the spiritual awakening of Europe and the loss of faith in old gods and goddesses. Several further Biblical reflections can be seen in the Zelda games but those have been touched on quite a bit by other theorists. These were some of the observations I made through the games and through my own Biblical study and I thought it would be fun to share. Take what you want from it, but as mentioned above, I see the world through the eyes of a believer.