During the era prior to the Dragon War, the Dragon Priest, Miraak, ruled the island of Solstheim from this temple. However, at some point, he rebelled against his dragon overlords, using his power to devour their souls to gain power over them. According to the locals, however, the dragons fought back, and a bloody and gruesome battle was fought at his temple, resulting in his defeat and the temple's ruin. 
In the Fourth Era, however, Miraak - who was living in Apocrypha, the realm of the Daedric Prince Hermaeus Mora  - began to take control of the people of Solstheim in an attempt to restore the temple to its former greatness and return to the island to his rule once again.
Temple of Miraak SanctumEdit
After discovering that the Temple is where Miraak's influence is coming from, the Dragonborn travels there seeking answers. Frea, a member of the Skaal, is found trying to discover what happened to some of her village's members, who are enthralled. She offers to team up with the Dragonborn in order to find Miraak inside the Temple. After defeating Miraak's cultists inside and advancing further into the ruins, the Black Book Waking Dreams is found. Upon reading it, the Dragonborn is transported to Apocrypha, where Miraak is encountered, along with several Seekers and a tamed dragon . After a small speech, Miraak then banishes the Dragonborn back to the Temple, and the next quest, The Fate of the Skaal, is started.
- A total of nineteen Dragon skeletons can be found around the exterior of the temple, however none are lootable, and, as the Dragonborn does not obtain souls from them, it seems likely that Miraak was the one who killed them, or that he was at least present when they died.
- A further three Dragon skeletons can be found displayed within the temple and the inner sanctum: the first can be found suspended in the Gatekeeper's room, the remaining two can be found in the Hermaeus Mora statue room, one can be found hanging from the ceiling covered in moss and the skull of the third Dragon can be found at the entrance to this room with (presumably) its wings arranged in the rooms center.
- The location symbol for the Temple of Miraak in the map in Dragonborn is unique in appearance.
- Draugr Deathlords can be found here at lower levels, allowing the Dragonborn to acquire Ebony Weapons at a much lower level than usual.
- The temple seems to be built up as the Dragonborn progresses through the story of the Dragonborn DLC.