Skyrim:At the Summit of Apocrypha

Quick Walkthrough
# Unlock the Bend Will shout and read the Black Book Waking Dreams.
# Traverse Chapters I to VI.
# Use the Bend Will shout to tame Sahrotaar.
# Reach the summit of Apocrypha.
# Confront Miraak and kill him.

Detailed Walkthrough
Chapter I
With the complete Bend Will shout at your disposal, it is now time to face Miraak. If you have not already done so, and are still in the Skaal village, take Epistolary Acumen from Storn Crag-Strider's body before entering, as it will not be there when you return.

Using dragon souls, unlock the remaining words of the Bend Will shout and read the Black Book Waking Dreams, where Miraak was first encountered during the quest The Temple of Miraak. You will be transported to Apocrypha, Hermaeus Mora's plane of Oblivion. Though this area is large, there's little of interest here now that Miraak has departed, only a few pods and tables along the walls. Walk down the path and up the staircase, where Chapter II will be accessible from a pedestal.

Chapter II
Ascend the stairs and defeat the two seekers. If you make enough noise, you can attract the attention of enemies far above you, but it is unlikely that you will be able to attack each other, so if you need to leave combat, just sneak until they stop looking for you. At the top of the stairs, a copy of the Smithing skill book Heavy Armor Forging is on a table to the right. When you get across the bridge, you can turn right and walk back along the narrow ledge to reach a pod. On the top landing, grab the book Boneless Limbs and go up the now-accessible staircase to reach Chapter III.

Chapter III
This next area may be a bit tricky to navigate, due to its maze-like structure. Defeat any seeker you encounter and make your way to the other end of the room, where the book Delving Pincers and a copy of the Alchemy skill book Song of the Alchemists lie. There is a pod across from the book pedestal and another down the stairs past it. After picking up Delving Pincers, return to the entrance, where the (previously closed) gate is now open. Activate the scrye and travel down the hall, where you can pick up a copy of the Enchanting skill book Catalogue of Weapon Enchantments from the table.

Be careful in the next room, where it is easy to fall off of the edge. If you activate the scrye in this room, a door will open off to the north, revealing a vessel with a bit of loot (there are also pods by the scrye and book pedestal here). Kill the seeker and traverse the narrow walkways to pick up the book Prying Orbs. With the book in your possession, the gate will open, and you can now continue onward to Chapter IV.

Chapter IV
Eliminate the seekers and walk down the stairs to either side of you. There is a pod on a ledge to your right. At the bottom, you will enter a hallway that has a fork to the right. Walking into either hallway will cause it to compress and summon a group of seekers. After you find that both hallways are a dead end, you can turn around and see that, where you had entered, there is a hallway that had not been there previously. Follow it to the next room.

Climb the stairs and pick up the book Gnashing Blades. This will open a second path to the right, directly across from where you entered. Continue down the hallway as it extends outward and take a left turn at its end. In this next room, follow the path until you reach a scrye. Activate it and go back to the same hallway you came from&mdash;it has shifted and leads to a room with a small pool of poisonous water. From the pool will rise a lurker. When the room is clear, activate the scrye to the left of the closed gate and go around a corner at the far end of the room (across from the previously mentioned closed gate). Here, activate the second scrye and examine the room next to it, which had been opened by the first scrye, for any valuables. You can find Chapter V through the gate opened by the second scrye.

Chapter V
The hallway will lead you to a large open room with a pillar in the middle emitting a green light. Defeat the seekers.

Surrounding the central pillar are four pedestals with inscriptions. On the walls near the eye and tentacle pillars, there are three pods. Place the four books that were collected in the previous Chapters on the appropriate pedestal:
Boneless Limbs is placed on the 'tentacle' symbol
Delving Pincers is placed on the 'pincer' symbol
Prying Orbs is placed on the 'eye' symbol
Gnashing Blades is placed on the 'fangs' symbol

Once all four books are placed correctly, the book located in front of the central pillar will glow. This will take you to Chapter VI.

There are three pods along the wall, before going to the central book.

Chapter VI

A copy of the Destruction skill book The Art of War Magic is located to the right of the entrance, while at the left, there is a pod with some valuable loot. The path will take you to a large open area surrounded by water. Kill the two seekers and approach the word wall, which teaches a word for the Dragon Aspect shout. Sahrotaar, a serpentine dragon, will attack you; however, you are tasked with taming it using Bend Will. Using the full shout on Sahrotaar (be sure to unlock all three words) will instantly tame him. He will land and offer to take you to Miraak. Mount Sahrotaar and fly to the large tower circled by dragons, but not before forcing you to fight enemies on another platform. After you kill the two Seekers and the Lurker, Sahrotaar will fly towards Miraak's tower. As you reach the top, Miraak will chide Sahrotaar for being so easily swayed by your thu'um. Once you land, approach Miraak, who will explain that his time in Apocrypha is done, and that although you are powerful, you are still subject to Miraak's power. Miraak will then conclude that the final key for his escape is your soul, and with it he will be strong enough to return to Solstheim.

thumb|right|The death of Miraakthumb|left|Miraak absorbing a dragon soul
The conversation will quickly end and the battle will commence. It is completely up to you as to how you would like to battle, either on the back of Sahrotaar or on foot. However, be careful of the other dragons trying to attack you. As Miraak's health is weakened, he will enter an invulnerable state and return to full health. Each time he regenerates, he will sacrifice a dragon: first Kruziikrel, then Relonikiv. The third regeneration will lead to Sahrotaar's demise, as Miraak absorbs his soul, too. With all three dragons eliminated, you can deal the final blows to Miraak. When his health is low enough, he will move to the center of the area in an attempt to escape. At this point, Hermaeus Mora will intervene, claiming that Miraak can hide nothing from him in his realm. The Daedric Prince then impales Miraak with a tentacle, and explains to Miraak that his death is insignificant, as he has found a new Dragonborn to 'serve' him. As Miraak dies, he wishes upon you the same fate he is about to suffer, and then disintegrates into nothing but bones as his soul departs from his body and is absorbed by you.

For Miraak's death, you will be rewarded with at least six dragon souls (additional number of dragon souls is equal to the number of dragons you've killed in the plug-in, regardless of whether their souls are stolen by Miraak or not) and you may loot his body for his equipment, as well as the bodies of the dragons. Reading the Black Book Waking Dreams will allow you to gain access to your skill trees (see the notes section). Read the book once more to exit Apocrypha. 

 

Achievements
One achievement is unlocked when you complete this quest:
 
Reaching the end of Waking Dreams counts as one of the five black books for this achievement:
 
If this is the first time you've fully traversed Waking Dreams you may earn the last word of the Dragon Aspect shout and thus this achievement:
 

Notes
If you fully traversed Waking Dreams before this quest, you will be returned to Chapter VI, where Sahrotaar will be waiting for you. You must then use Bend Will to tame him and continue the quest, as above.
At the end of the quest, you will have access to different portals (one for each skill) which allow you to clear and regain any perks in that skill tree, at the cost of one dragon soul. You remove all perks from a single skill perk tree and can use these reclaimed perks on unlocking any perks you wish, including perks taken from said perk tree. By reading the Black Book Waking Dreams, you can return to Apocrypha and alter the skill trees whenever you wish.
Completing this quest also cleanses the Tree Stone, granting you access to its power.
If you are defeated during this quest, before confronting Miraak, you will be transported back to where you initially read Waking Dreams. You will return to the chapter you last accessed when re-entering Apocrypha.
If you return to Skaal Village after completing this quest, Frea will inform you that the Oneness of the land has been restored, and that the Tree Stone is now free. She will also warn you not to become involved further with Hermaeus Mora.
If you return to Tel Mithryn after completing this quest, Neloth will check that you have no indications of Hermaeus Mora's permanent influence. After satisfying himself that you don't, he will direct you to find more Black Books, if you have not found them all already.
In order to travel to Apocrypha by reading Waking Dreams, you must be on Solstheim. If you try to read the Black Book in Skyrim mainland, nothing will happen and a message will pop up, saying: "A vision of Solstheim swims before your eyes and then is gone." The same situation also occurs with the other Black Books.
Unlike the other sections of Apocrypha accessed through Black Books, you can never return to the first five chapters of this area after you defeat Miraak, so be sure to pick up any items you don't wish to leave behind before mounting Sahrotaar.

Bugs
 
Reloading a save from before the battle begins should fix this, but doesn't always work.
If reloading doesn't help, try hiding behind a big column of books. If you are a long distance from Miraak and out of his line of sight, and then wait a couple of minutes, he may re-materialize and attack you.
If reloading doesn't seem to help: if you can manage to kill all the dragons before wounding Miraak, then once you deplete his health, the fight will go right to the scene with Hermaeus Mora. However, this doesn't always work out this way.
 Create a new save at the point when all dragons are dead and Miraak is intangible and ignoring you. Quit and restart the game. Load the file you just saved. There is a short pause. Then Miraak calls out "Kruziikrel! Relonikiv!  Now!" There is a second pause. Then Miraak says "Ah, now we can finish this!" There is a third pause and finally Miraak attacks you in solid form and you can defeat him to complete the quest. Do not move around or otherwise try to engage him during the pauses. Wait for him. Note, Miraak might only pause once or attack without hesitation. Note this solution does not always work.
 Open the console, click on Miraak, and type   or  .
One cause of this bug may be that any of the dragons are stuck in flight and will refuse to land, making it impossible for Miraak to absorb their souls. Using Dragonrend on any dragon in flight should fix this. 
As a last resort, instead of attacking Miraak, mount Sahrotaar, then have him lock onto Miraak and attack him. Eventually Sahrotaar will land and attack Miraak on the ground. Each time Sahrotaar is about to finish its attack, command it to attack Miraak again, which will prevent it from taking flight. Eventually, Miraak will kill Sahrotaar, absorbing its soul and throwing you to the ground. Immediately use the Bend Will shout and mount the second and third dragons, then repeat the above steps until all three dragons have been killed. Miraak should be engaged in combat again.
 
 Using the console command   will bring you to the place that Miraak fell to. It is right below the place you fight him, on standable ground. You can also use the command   to turn off collision to clip through the floor, loot his corpse, then move back up to the surface. Use   again to turn collision back on.
 
This may be due to mods (or load order) that affect dragon soul absorption.  See discussion tab.
This may be due to not killing any dragons after starting the quest line as it never triggers him to steal dragon souls from you (which is possible if you have a few dragon souls saved up to use along the way).
 
Exiting and restarting the game may fix this.
 
 
This may be due to the Seekers falling from the walkways on the upper levels, and sustaining fatal fall damage.
 
Ensure all three words of the dragon shout for Bend Will are obtained and unlocked.
The quest may not have been entered into the journal, despite completing the prior quest.  Use the console command   then walk around the locked gate to trigger the next objective and he should arrive.
 
 
 
 
Reloading a save may fix this. 
 
 One possible solution is to use the   and   console commands on Miraak. He will then be impaled.
 Using the fire breath shout on the central slime pool may fix this.
 Use these commands to end the quest:   followed by  . The 580 stage of the quest is what raises the new altar from the pool of liquid. The raising of the altar will sometimes bring up Miraak's body if he is stuck under the liquid. This is also the stage that causes the glowing skills icons to appear.
This or the following setstage fix may cause the combat music to become stuck, looping forever. In this case, entering the command   should solve the problem.
 
Using the console to spawn a new book, and reading the new one should fix this.
 
Fast traveling should fix this problem, although shadows may still be affected.
 
 
 
 If this happens, you may use the console command   to warp to the beginning of Chapter VI.
 
This is fixed when Miraak becomes low on health and absorbs Sahrotaar's soul.

Quest Stages