This is the most important part of Hyrule history: Getting the Master Sword out of it's pedestal to defeat the ultimate evil. Though there are many forms, it's probably the most important weapon in taking down Ganondorf. He's not here now so you could breathe a sigh of relief for the moment. Note that you can only choose Link for the first time. But the next time, you can choose anyone else to fill in that role.
Ghost Whisperers and Goddess Statues
You have only Link for now. It's worth using the Fire Rod for this level. Anyway go directly east to the church which is currently closed. Go north and south and directly west to confirm the locations of the Goddess Statues once the ghost soldiers appear.
Protect everyone! Including Midna, Lana, Impa and Darunia since they might be attacked by summoners. Activate the owl statues on 3DS and Switch version to make travelling easier. Also protect Zelda from danger as having no health will cause her to flee and giving it a game over.
Evil Lana to battle!
Once all statues have been activated by some time, they wonder why the ghost soldiers were still around. Go to the middle of the map, east of where Zelda is and you might find Lana between the checkpoint officers. Defeat her like you did with any other warrior you fought so far in this game. Doing so would end the ghost control and they will disappear.
Link versus Wizzrobe
You can now go in the church now. Clear out just the leaders and their base areas before getting the "Master Sword". Wizzrobe will come out, fist of fury! Or magic fury. Again, it's a no brainer but Wizzrobe will disappear for a while and magically sends an army into this level.
Zelda in Distress
You're going to have to run to her location and start defending her until she reaches the church on the east side of the area, by the entrance. Keep Lizalfos, checkpoint officers and an enemy base away from her so that she can keep moving. Once she's there, you have one more thing to do left.
Wizzrobe last stand
Use the ocarina if you turn the statue on the west central side on in 3DS and Switch version. The Wii U version has you force your way to Wizzrobe location on the opposite side, the west side where Impa was temporarily protecting the Goddess Statue. Battle him once more and he'll reveal the location of Cia: The Temple of Souls. Though Wizzrobe will resign to his ring, the chaos is still far from over.