After you've learned the complete Bend Will shout, you can read the Black Book: Waking Dreams. Once you are inside Apocrypha, walk straight ahead and up the platform to find the book for Chapter 2.
You will be indoors now. Go up the stairs to your right and at the top, you'll be on a ring around the outside of the room. You'll bump into a Seeker on this ring so be ready for him to materialize. Keep going around the ring until you find a bridge to your left that crosses the gap. Go across and up the stairs at the end. At the top of the stairs will be a book. Pick up the book "Boneless Limbs" and head back across the bridge.
On the far side, go up the stairs to the left. You won't see the door now but there was originally a door here that was opened when you picked up the book. This will happen in each of the Chapters here. Go through the now open doors and start Chapter 3
You're in a hallway. Go down the end and go left. Be careful, however, because there will be many small goo pits around here where tentacles will come out and attack you. There are also a couple of Seekers in this area as well. This room consists of three horizontal hallways that you can move between.
First go left and at the end turn right twice to go down the middle hallway, at the end, turn left twice and go up the stairs. At the top, you'll see a book to your left looking over the hallways towards your entrance. Pick up the book "Delving Pincers" and then head back towards where you entered this area. Don't read the book at the end of the hall as this will bring you back to the previous chapter. However, if you watch to the left as you approach the book for Chapter 2, you'll see a hallway.
Go into the hallway and activate the Scrye beyond. This will cause the hallway to stretch until it hits a ramp leading up. Take this ramp up and you'll be left at an intersection. Head right and you'll enter a large round room with a few parts around the outside connected by a large central bridge network.
On the left will be a Scrye so use that and then go out to the bridges in the middle. There are many paths out from the center but you are looking for one that leads to another book, Prying Orbs. When you get to the center from the Scrye area, take the first left and you should find the book. Come back to the center and take another left to be lead to the next chapter.
Standing on a platform, if you go to the edge and look down, you will see a bunch of stairs leading down. There will be a few Seekers here so be on your guard as you descend. At the bottom right side of the area will be a long hallway. Walk through the hallway but don't be surprised when it shrinks in on you. When it does this, try to take the other path. This will fail as well. When both have failed, try to head back to where you entered the hallway to find that you are somewhere else now.
Almost as soon as you exit, watch for a couple of Seekers to your left. Kill them and then take the stairs that lead up directly across from the hallway you just came out of. At the top of the stairs, take this next book, "Gnashing Blades". Go back down the stairs and hug the right wall as you do so. This should leave you in a new hallway that is just across from the original hallway.
Inside, walk through it and straight past the large lamp post. This time, the hallway will stretch. When it has, take a left at the end to come out in a new area. There are a couple more Seekers out here. Kill them and climb up the stairs by where they are. This path will take you across a bridge and ultimately up to a platform with a Scrye at the top. Hit the Scrye and head back down.
At the ground floor, you'll find a new doorway across from Scrye. In this next hallway, go to the end and turn left. You'll find yourself in a large room with a pool of goo in the middle. Cross this room diagonally and you'll find another open doorway into another small hall section. A Lurker will come out of the goo. Kill him and then find the large door not far from the goo. Looking at this door, turn left and you'll find a Scrye near the lattice wall. Activate that and you'll see the door open in the small hall beyond. Go into this hall but watch against the right lattice wall for another Scrye just before the room you opened. Use this to open the large door in the previous room. Loot the chest ahead if you like and then head back to the large door.
This large door will lead you to Chapter 5
You'll start off in a book cave. Go to the end of the cave and you'll come to a large room with a central pillar and four spokes. Between the spokes on the outer rings will be platforms with pedestals on them. Each of these pedestals will have a picture on it that tells you which of the books you picked up should be placed on it. Watch out for the Seekers in here.
The first Pedestal that you see will be a mouth with large teeth. This is Gnashing Blades. To your left will be a pedestal to your left will be Prying Orbs. The pedestal left of that (opposite where you entered), is Boneless Limbs, and the last one will be Delving Pincers. When you've placed all four books, a fifth book will appear on a pedestal in the middle of the room. This book will lead you to the final chapter.
When you land, go around the books blocking your path and head outside. In the distance will be a couple of Seekers and an odd looking Word Wall. Rather than being carved into stone, it's written a wall made of moving paper. Learn the next level of the "Dragon Aspect" shout. A dragon will appear behind you and hover for a moment. Use your full Bend Will shout to tame him.
When he lands, climb on board and he will take you to Miraak. You don't actually have control of the dragon's flight will riding but you can use him to help you fight. The game will instruct you on how to lock on to enemies and how to use his breathe attack. If you need more information, check the help section of the menu.
He will first take you to a platform with enemies on it and let you practice the dragon controls on them. When you've taken them out, he will fly on and you'll be prompted to land. When you do, he'll drop you off at the summit of a Apocrypha.
The fight with Miraak isn't anything of note at first. He has the abilities you would expect him to like several offensive shouts and various ranged magic attacks. Close in he also has a sword that he can use. It is important to be careful however because he can deal some serious damage and this fight will take longer than you expect.
When you lower his health to about 1/4, a Dragon will come down from the sky and land. He will then kill it and absorb the soul to heal himself. He will do this three times and if you aren't careful, the dragons may also attack you. As long as you are vigilant about your own health and keep moving, you should be able to survive. If you need a moment to collect yourself, it may be best to go down the stairs the he came up for a moment. You won't get a whole lot of protection but the few seconds may save your life.
After the cutscene plays out, loot his body and those of the Dragons if you like. A structure will rise out of the center of the ground. Inside will be another reward book. If you open it up, you'll find that you can reassign the perk points of any skill. Do so if you like or use the book to leave. You can always return later to use this book again.
Congratulations on once again being the only Dragonborn in Tamriel. You'll left in the Skaal village and the only thing left to do is to talk to Frea.