After completing The Egyptians' Fate and sparing Khonsu, as well as The Winged Sun, returning to Odaiba will let you hear a request from Isis as she reveals Khonsu's Knowledge is in Miyazu and he has been keeping her alive for a long time, but now he's decided to go for a more decisive way to help her, and he needs to be stopped, so we're off to the Fairy Village!

Naturally, you'll have to fight him, and the level 82 Deity can put up a decent fight! He'll call for backup as the battle starts, summoning Anubis and Thoth, and then attack you with Fire, Light, and Almighty attacks so try to avoid weaknesses to these elements (Unlike me with Fire).

Take down his summons first as they can be an annoyance and he won't resummon them, then turn your attention to the main boss, Khonsu Ra is immune to the two elements he employs, but is weak to Ice which you can exploit for more Press Turns. His Magatsuhi Skill is Mahamaon, easily nullified, and if you see him using Mesektet's Path, don't attack unless you're sure you can finish him off.

After that, one last choice remains, you can kill Khonsu or spare him by either stopping him or doing nothing. Either way you'll get two Large Glory Crystals and unlock both Khonsu and Khonsu Ra for fusion.

Timestamps:
0:00 The quest begins.
7:38 Khonsu-Ra fight.

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