Amaterasu and Issun first learn about the Day of Darkness from Kai, who explains the urgency of the day. Should the blizzard that was ravaging Kamui continue to freeze the land by the time of the eclipse's arrival, Kamui would be completely frozen, and no living thing would be able to survive the day. The only person who could possibly save Kamui from being frozen over was Lika, Kai's little sister. Unfortunately, Lika had gone missing by the time of the game's events, and it was up to Amaterasu to find her before the arrival of the eclipse.
Amaterasu began her search in Yoshpet, the forest of deception. There, she came across the village of Ponc'tan, whose residents recalled a mysterious girl vanishing into the Spirit Gate, a mystical artifact residing at the edge of the forest. Amaterasu journeys to the Spirit Gate, and after a series of events, manages to recover Lika, but upon returning, she was frightened at the sight of the Day of Darkness beginning.
After rushing back to the edge of Laochi Lake and defeating the terrors that lurked within Wawku Shrine, Lika performed the Volcanic Incantation, causing the twin volcanoes of Ezofuji to erupt, and warming the land of Kamui. The people of the land did not have to fear the Day of Darkness any longer.
Or so they believed. The Day of Darkness finally began when Amaterasu boarded the Ark of Yamato and confronted Yami, the ruler of darkness. Strengthened by the solar eclipse, Yami managed to strip Amaterasu of all her Celestial Brush techniques, rendering her a normal, white wolf, broken and helpless. Despite this, Amaterasu proceeded to fight Yami in a long and grueling battle between the Sun god and the Emperor of Everlasting Darkness, regaining her brush techniques as she went. Eventually, she managed to knock Yami down, only to have him destroy her brush techniques and assume his true form. Just when things started to look bleak, the voices of everyone in Nippon could be heard, sending Amatersau their prayers. Issun had created a swell of faith in the people of the country, and with this faith, Amaterasu proceeded to annihilate Yami. With the ruler of darkness defeated at long last, the light of the sun filled the land once more. The Day of Darkness had come to an end.
The Day of Darkness is considered the final climax arc of the game, and signifies a point of freedom for the player should they not immediately board the Ark of Yamato, which from then on is the point of no return. This is most significant in the actual eclipse's phenomenon affecting the overall setting; if Amaterasu returns to any other areas in Nippon after defeating Lechku and Nechku, with exception of Kamui, daytime skies will be much darker, and the livelier renditions of overworld themes will not play when the day passes into the afternoon. Kamui will still boast its livelier themes, but its skies will showcase the eclipse. All sidequests in the game come to their penultimate end by this point in the story, which is further incentive for exploration and to not yet board for the Celestial Plain.
- Despite being a "day of darkness", Amaterasu can wander around Nippon for as long as she pleases before the actual eclipse occurs. Day and night continue to pass and Sunrise and Crescent can be used to change the time. However, Amaterasu cannot prolong the eclipse, speed it up, or prevent it from happening altogether.