This game takes place in the Child timeline and comes after Twilight Princess.
The game starts off with Link at Lon Lon ranch sleeping (as usual) on a pile of hay. He is abruptly woken up by a cow licking his face. Malon, who is looking on, laughs and tells Link he overslept, and needs to deliver a shipment of milk to Hyrule Castle town. Link immediately gets to it, knowing Talon will be mad at him if he doesn't. This is when you gain control of Link. During this sequence, you must escort the cart to Hyrule castle while fending off some low-class enemies like bokoblins, keese, etc. with your wooden sword. After fighting off some enemies, you make it to the town where you stop and read a message board saying:
'The princess has decreed that he who bears the mark of the goddess Farore must come to the castle immediately, so we may be prepared if ever the evil Ganondorf spoken of in the ancient texts returns.'
You look to your left hand, which bears the mark of the Triforce of Courage. Suddenly, two soldiers come up behind you and notice your mark. They immediately take you to the castle, and to Princess Zelda who recognizes your features as similar to the Hero of Time. Zelda proceeds to explain how she read ancient texts on the events in the era of the OoT and TP, and did not want to meet with a terrible fate like those Zeldas almost did. Thus she decided to search for the newest incarnation of the Hero of Time. She says that she is giving a speech later that day and wants you to guard her. She proceeds to give you the hero's tunic, Hylian sword, and Farore's Shield (wooden shield). now, you are free to explore Hyrule castle, where you must complete some tasks for various npcs (similar to TP's second day). After doing this a guard comes to you and announces that the princess is about to give her speech, so you take up your post at a pillar guarding the entrance to the balcony on which Zelda is giving her speech. Suddenly, you see a dark thing move out of the corner of your eye, and a figure dressed in a dark cloak bearing the Sheikah symbol comes into your line of sight and draws back a bow. Before you can get out your shield, he nocks an arrow and fires it into your heart, killing you (this is a special arrow which sends you to the underworld instead of giving you a game over) You arrive in the underworld as a soul. Before you, there is an obsidian temple, The Temple of the Dead, the first dungeon of the game.
The first half of this temple is you essentially learning the ropes of Ghost Link, who can possess things, cause a trail of ethereal ice, turn invisible, phase through certain objects (and scramble the circuits of certain enemies), and other abilities which will be shown later. Eventually, you get to a chamber housing a Stalfos, the first miniboss. the Stalfos has a blade which can harm link. To defeat the Stalfos, you must turn invisible, so it goes back to being a dormant pile of bones, then possess it and mash A to fight for control. afer doing this three times, you gain control of the Stalfos completely. You can now use this corporeal form to solve other puzzles requiring a body, such as pushing blocks, holding down switches, etc. Also, as a reward for beating the Stalfos, you get the Skull 'Rang, which is essentially just the Boomerang. You must use this to solve various typical boomerang puzzles. Eventually You get to the boss chamber, and see a giant skull in the center (think Stalchampion from TFH) with some bones surrounding it. Suddenly, a flaming poe rushes into it, possessing it. This is Infernal Spirit: Blazebones. He attacks by using femurs to whack you and breathing fire. When he is breathing fire, he charges up his attack by opening his mouth and sucking in air. When his mouth is open, you must boomerang-target his Jawbone hinges and cut off his jaw. This will allow you to get to the poe lantern inside his skull, the poe's weakness. after dong this a few times, he grows a fiery mohawk, and abandons the fire breathing attack fo a new one, the rib boomerang (again, think Stalchampion) which you must dodge. He then proceeds to spin this head vertically like a flaming wheel, and chase you in that fashion. you must then leave your Stalfos body and make a trail of ethereal ice, then lead Blazebones through it, putting out the fire and allowing you to 'rang him. After doing this a few times, Blazebones is defeated, and the door to the next room opens. You enter to see a flute carved to look like a spine with a skull at the end, the Skull flute. there is also a stone tablet with song directions. upon playing it, you are notified that you have played the Serenade of Souls, which allows you to separate your soul from your body and use it to solve puzzles.