Dragonborn - At the Summit of Apocrypha

Once you have the Bend Will Shout unlocked read the Black Book Waking Dreams and you will be transported to Apocrypha, Hermaeus Mora's plane of Oblivion.

Follow the paths and complete the chapters.

In chapter 6 use the shout on the dragon Sahrotaar which will tame him. He will land and offer to take you to Miraak. Fly Sahrotaar to the large tower circled by dragons. As you reach the top, Miraak will scold Sahrotaar for being so easily swayed by you. 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.

The conversation will be over quickly and then battle with Miraak will commence. Miraak is pretty tough as his health is weakened, he will enter an invulnerable state and return to full health by sacrificing a dragon, of which there are three, so be prepared.

When Miraak's 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.

Return to the Skaal and tell them all is well.