This page highlights the major main quests of the game, there are 23 in total and some of these may contain spoilers. You can see walkthroughs of the main part quest by IGN by clicking on the pictures, and an overview by clicking the quest title. (Excluding the Regional Phenomena as that has more than one total main quest.)
On the Great Sky Island the Temple of Time dominates the island, however it's unable to be opened. The ghost of the ancient Rauru appears and talks to Link, saying that the door won't open as Link's new right arm is filled with evil from years of sealing Ganondorf and must be purified by going to all four Shrines of Light. After visiting each one Link gains the ability to use Ultrahand, a building tool. Fuse, a tool that fuses objects to weapons to make them stronger. Ascend, to phase through up to the surface above Link, and finally Recall, which allows Link to rewind some objects. After this Link enters the temple and goes down to Hyrule.
After going to Lookout Landing, Purah, the leading scientist tells Link that every major settlement that is non-Hyrulean is suffering somthing and Link must veture to each one to help the settlements. From Lookout landing the northewest Rito Village is suffering a visible blizzard and a massive cyclone rages above the village. To the northeast the Goron City where a new type of rock has been found and when eaten, causes the Gorons to only want that, only leaving the children and oldest not in such trance. The east, Zora faces massive pollution and they form the source of the majority of the water for Hyrule and if lost everyone would get sick. To the southwest, Gerudo Town faces large sandstorms and creatures known as Gibdos, the town is having trouble and is attempting to keep everyone safe however they are in a bunker.
Map of the Hyrule Kingdom, Estimated Time ( ??? Hours )
At Rito Village a storm has been raging for a long time. This storm is supported by a raging cyclone. An ancient song depicts that in the worst ties of the village, ships will descend from the skies to save the village. Tulin, a young Rito warrior who is the son of the elder Teba, really wants to investigate however isn't allowed to. However he and Link sneak off and climb to the top of the cyclone and find the Legendary Stormwind Ark suspended inside the cyclone. They then must fight a massive monster known as Colgera, (it has a really good soundtrack) and it is the cause of the blizzard. After defeating it Tulin is shown as the Sage of Wind and the cyclone clears away.
In the Eldin region, the mining company has discovered a new type of rock. Marbled Rock Roast, and since Gorons are able to eat rock theyh eat it and it makes their eyes glow purple and all they want is more of it. Yunobo, the head of the company has some sort of mask on and it seems to be making him unlike himself. Link confronts him and breaks it and Yunobo says princess Zelda gave it to him. Yunobo and Link climb to the top of the only volcano and highest point in Hyrule, Death Mountain. They confront a rock monster and fall into the depths of the mountain and find the Fire Temple. They fight a being made of Marbled Rock Roast and it makes the Marbled Rock dissappear after it is defeated. Yunobo awakens as a sage and the mountain stops spewing out Gloom.
The Zora have been dealing with a pollution problem. If they let it go on the whole kingdom's water will be polluted, therefore they have been trying to contain it. Link goes there and cleans up some of the Mud falling from the sky and meets with Sidon, the Prince who is single-handedly keeping most of it from spreading. They travel into the skies and reach the Water Temple and defeat the Mucktorok. The one polluting and the mud disappears. Sidon then finds out he is the Sage of Water and Zora's Domain is now safe.
In Gerudo Desert, large sandstorms rage across the desert filled with creatures called Gibdos, which are seemingly immune to all attacks. Gerudo Town, the major settlement is infested with them and everyone is in a bunker below. There, Padma tells that Riju is practicing for protecting the town. As Link meets up with Riju, Link defends the two settlements of the desert from the Gibdos. Riju informs of a myth and they find three red pillars, and light them together to form a triangle and in the center the Lightning Temple rises. The Queen Gibdo blocks the entrance and after beating them they retreat into the temple. Defeating them a second time, Gibdos seem to vanish and the sandstorms as well. Riju awakens as the Sage of Lightning and the Gerudo are safe.
Spirit Temple, enroached in darkness Estimated Time ( 6 Hours )
Finally after finding every sage, it is revealed there is a fifth sage, however no one knows where it is and the sages and Link set out to find so. At Kakariko Village there is mysterious rings that are investigated, one hinting that in the southeast, the Faron region hides the 5th sage. After venturing and finding a couple pieces of armour, Link manages to make in to the lightning storm above the region. Inside Link traverses the floating islands and finds a strange mask at the end which brings him underground. Down in the depths the mask says that they are the fifth sage however they are a spirit as their body was destroyed. Mineru, as their called tells them to construct a robot body for her and Link builds one and they then venture to the Spirit Temple, where they fight the Seized Construct and Mineru reclaims their spot as a sage.
Link now with every Sage must reclaim the Master Sword, as Mineru says that Zelda knew her and she tried to restore it to normal. However she does not know where it was and suggests going to the guardian of it, the Great Deku Tree, howwever the citizens of the Lost Woods, the Koroks haven't been able to enter, and Link manages to take a shortcut through the depths. There Link sees the Koroks in the forest are unable to move and the Deku Tree can't talk. Link dives down into the Deku Tree's trunk and finds a Phantom Ganon. Defeating him cures the forest the The Deku Tree says the sword is on the Light Dragon. One of the four dragons the fly around the map and the youngest one. After climbing onto the dragon Link collects the Master Sword.
Hyrule Castle above Gloom's Approach, Estimated time (1 Hour)
After all this preparation it is finally time to confront the source, Ganondorf. Link dives under the Hyrule Castle and enters Gloom's Approach. After venturing to the bottom Link fights Ganondorf's army and if he didn't complete any sage quest, their respective boss. After defating his army Link engages in a battle spanning from the Depths to the Skies.