Before heading into the temple, you can keep talking to Frea and ask her more about the Skaal and about Miraak. Sometimes Cultists will attack and interrupt the conversation, afterwhich Frea appears to have vanished, but in fact she just went into the Temple of Miraak on her own. Go down the spiral path, and enter the temple yourself, you will find Frea there.
After entering the temple, go down the tunnel. Frea suggests checking the rooms for supplies before heading further into the temple. Turn right into the first chamber and loot stuff from the skeletons and burnt corpses there. There is another room with some table in it and more items. Go back into the main tunnel and follow Frea into a supply room full of potions and a chest. Frea is sitting outside on a bench waiting for you. Go north, deeper into the Miraak temple. Upon entering a circular chamber, you will be attacked by cultists. Kill them and loot anything of interest in the room.
Frea advises you to be careful in these ruins. Traps can be anywhere, and there will likely be many. Miraak was trying to take power here, and protect himself in the process. Exit the room to the north, watch out for the trap in the corridor (jump over any glyphed pressure platform on the floor). Go down some stairs and activate the chain to the right of the gate to open it.
Enter a big room with lots of cages. Frea tells you to look up, she thinks she saw something. But the stairs are knocked out. Frea has no doubt you can find a way up. You never know, you may find something of value up there. This is a PUZZLE.Temple of Miraak Throne Platform Knocked Out Stairs Puzzle Solution
This is how to get up the Knocked Out Stairs to the area with the throne in the Temple of Miraak
From the very bottom, start going up the stairs. But do not turn left towards the throne, instead turn right. See screenshot below for help:
Then, see the SKELETON on the floor. There is a big stone archway near it. Climb up the curved archway:
Then, just jump from the archway and onto the throne area:
You land on the Throne area, which has some valuable items as well as a chest with more loot. The chest might sometime contain a Stalhrim Weapon. After you are done looting the area with the throne, jump back down to the main area.