Okay, Link's first adventure on the DS! Yay!
I'm going to assume you've already set up your gameplay Options and watched the opening cutscenes, so let's get right into it.
The Fairy that wakes you up is Ciela, and unlike Navi and Tatl she actually does things for you (unfortunately, her usefulness right now is limited to showing you where the stylus is touching the screen). Explore the beach until you find her "grandpa's" house; inside, Ciela convinces Oshus (the old guy) to tell you where to learn more about the Ghost Ship.
Leave the house and an earthquake starts. Jump off the ledge and head to the east; Oshus said that Mercay Island's town is to the east across the bridge. And, as would be expected, the earthquake knocked out the bridge. Fantastic.
- Ya know, Ciela, the bridge would still be there if we'd just gone to town first, but noooooooo, we had to go see your "Grandpa" first...
Go back to the west and look for a path leading north. Head up the path to make Ciela scream for you to "look out" because of the "monsters". There's no point in going forward, so go back to Oshus.
- The "monsters" are Red ChuChus. Ciela won't force you to turn back, and you can actually run right by the little bastards. But the trail will block you; you'll run into some trees that you can't pass. We need a sword to cut the trees down and continue.
He scolds Ciela for taking the north road, and tells you to not even think about going north because of the monsters. Dude, they're ChuChus; globs of Jell-O with weird faces. If that's a monster I'd hate to see what a real threat in this game would be. Anyway, Oshus tells you that he's sure someone will be around to repair the bridge eventually, so we should just wait.
- Zelda fans will know that "eventually" translates to "after you no longer need it to happen". So the bridge won't be fixed until we've already gotten to town.
Leave the house and go east to find a cave behind some barrels. Go inside and examine the sign by the stone door; write a 7 on it to open the door. Inside the chest is Oshus's Sword! Yay, we can stab things now!
- It's picky about the shape.
Now we can go back to the trail and get to- ah, crap, we're caught. Oshus is waiting for us outside the cave. Now he's gonna start yelling at us and then he'll tie rocks to our feet and- teach us how to use it properly? Okay then...
After the sword tutorial, head back to the north trail. Roll into the first large tree you find (see the weird statue to learn how) for a Red Rupee (worth 20), and continue to the cave. Move the boulders out if your way, kill some Red ChuChus, and push the blocks to the east and west to find some more rooms; they both have Keese and a sign, and the east one has 20 Rupees in a chest.
Return to the center room and pull the levers on the north wall in this order: middle left, far left, far right, middle right. This causes a Small Key to drop from the ceiling and land in the center of the room (pulling them in the wrong order makes a bunch of Ropes fall). Use the Key on the door and head up the stairs.
In the next room, locate the pushable block to the far left. Move it so that it's blocking the nearby Rat hole, then backtrack towards the locked door. A Rat will run out of the right hole and try to run around to the left hole; follow the little bastard and kill him as he tries to run back, then grab the Key he leaves behind. Unlock the door and run past some Keese to reach the exit.
- That Rat gave me a hard time before I figured it out...
We're finally in town! Our first stop should be the store (southwest building); if you've gathered up 80 Rupees already, buy the Wooden Shield (which doesn't burn for some reason). That's pretty much the only useful thing you'll find at the moment; the red gem (a Power Gem) they're selling will be important later, but you're very unlikely to have 500 Rupees by now. Head outside, grab a Cucco, and go to the ledge near the shop; jump across the gap and go up some stairs to find a chest with a random Treasure inside.
- Treasures are kinda useless right now, but eventually a store will open on Mercay Island where you can sell them.
Head to the east side and talk to the guy next to the boat there to learn that the boat's owner is probably at the town's bar. So head over there, only to find out that he's not there either. Linebeck went over to the Temple of the Ocean King. And from what these people are saying it's not a very friendly place. Oh, joy.
- Piece of advice: if you use an AR with your DS (I have to because it won't recognize the game without it for some reason...), never set it down on your laptop while you're typing. The game will freeze and you'll have to redo everything since your last save.
Head north out of town and make your way to the west; on the way, roll into the northernmost tree to find a Big Green Rupee (worth 100 Rupees!). In the next area, head west (ignore the cracked wall; we'll do that later) and then north to find the Temple of the Ocean King.
Ciela's creeped out by the skeletons on the floor in here, and for good reason: they come to life and attack!
...Just kidding. Run through to the next room. You'll see some guy trapped behind some spikes, asking you to help him; Ciela identifies him as Linebeck. Linebeck claims that the only reason he needs help getting out is because he "sprained his ankle". Oh well, let's help him out; we need him anyway.
But, right as Link's about to leave the glowing purple tiles on the floor, Linebeck remembers to tell you about the curse that'll suck your life away. If you're not standing on the purple sections ("safe zones"), you'll lose 1/4 Heart every 2-3 seconds.
Don't let the health loss scare you; the room's layout makes it practically impossible to die. Leave the safe zone and run to the left to find another one. Step on it, then leave it and go north to find a crystal switch; hit it to free Linebeck. Who promptly runs to the entrance of the room. "Sprained ankle" my ass...
Go to him and watch the cutscene (Linebeck's one of my favorite Zelda characters...), and Linebeck gives you the Key he found so you can go further into the temple (honestly, I don't know if Link's abused more in WW or PH).
Open the locked door near the switch you used and go to the northwestern safe zone to find another switch. Activate it and quickly run east to a switch in the northeast corner; hit that one to open the door to a large chest, where you'll find your first Sea Chart! Run back to Linebeck and- wait, where'd he go?
You'll find him outside the TotOK. And he steals our Sea Chart. Head back to town and go to the docks, where you find Oshus and Linebeck talking. Oshus hands you the Sea Chart, mocking Linebeck for not being able to find its secrets and telling you that a section of it is "a little flaky". Rub the southeastern island on the map to reveal an orange symbol. That's where we need to go: the Isle of Ember.
Isle of Ember
Talk to Linebeck when you're ready to go; he'll give you a brief tutorial on navigating at sea. Set a course for the Isle of Ember. You'll probably find a Golden Frog jumping out of the water just to the south; ignore him for now, since we can't do anything with him yet. Just enjoy the trip.
At the Isle, find the fortune teller's house and go inside, then go down into the basement. Kill the Octoroks that appear and go to the blue door on the right; blow into the DS's mike when Ciela tells you to call out. Astrid tells you to find her assistant so you can open the door. So leave the house and go to the east end of the island. When you find Astrid's assistant, you'll learn that he died. His soul will tell you how to open the door, though: you have to mark the island's 3 torches on the map by the door. So go back and mark the three torches: the southernmost house, the island to the east of Kayo's corpse, and to the right of the northern island.
Astrid's free, and she tells you to bring Linebeck to her so you can have your fortunes told. Blah, blah, go to the Temple of Fire, bla- wait, what? She unsealed the door leading to the summit of the mountain, so now we can get to the Temple of Fire. Yay.
Head back towards Kayo's body until you find a door; open it and head up the stairs behind it. You'll encounter more Tektites on the way, as well as some electrified Yellow ChuChus (either ignore them or wait for the charge to disappear before attacking). When you get to a pair of candles flanking a door, blow them out with the mike to open the door to the Temple of Fire. Don't go in yet; instead, go past the door and keep going up the mountain to find a chest with 20 Rupees. Now go into the temple.