Undefined Fantastic Object - Story

Story

Rumors have been spreading throughout Gensokyo since early spring about a strange flying treasure ship. Figuring there must be something up there regardless of the rumor itself, and aided by Sanae Kochiya, the girls take off into the air to find it and plunder its treasures.

During the high-speed chase of the "UFO", the player confronts Nazrin, who has come from the flying object and is looking for something in particular. She insists that there is no treasure ship at all. After that, the player runs into Kogasa Tatara, whose role is nothing else but to scare the girls.

As the player finally catches up to the ship, Ichirin Kumoi and her familiar Unzan appear, complaining that all sorts of fairies and humans have been pestering them. She explains that the ship isn't a "ship" at all, but rather some kind of remodeled building given the power of flight. She also mentions that she's trying to revive a certain someone. The fragments - the UFOs that the player has been collecting - are necessary for this purpose, but rather than handing them over, the player instead defeats the pair and enters the ship.

Inside, the player runs into a strange flying object that promptly attacks, then leaves items. Disregarding this, the player then finds Captain Murasa, the youkai ghost captain of the ship. She tells the player that the ship is headed for Hokkai, located on the outer edges of Makai, a world connected to Gensokyo. Since the player entered with enough fragments in their possession, the ship has already begun to enter Hokkai.

Before very long, just outside Hokkai, the player runs into Nazrin again, who has found what she was looking for - the Vaisravana pagoda. After defeating her a second time, Shou Toramaru appears. Now that both the pagoda and the fragments are together, the revival can begin. Shou tells the player that they are trying to revive a "saint" who has been sealed for many years - a person who helped both humans and youkai, and was punished because of it. After defeating Shou, the player opts to help revive this person, since they're already there and everything.

The final confrontation happens deep inside Hokkai, where Byakuren Hijiri has been unsealed. The player's job is to exterminate youkai (or, in Marisa's case, to prioritize protecting humans), so Byakuren disagrees - she is an ally to both, and treats both equally. The player defeats Byakuren in a long battle, and the story ends on peaceful terms, as she and Murasa cruise around Gensokyo in the ship for a while before settling down and rebuilding Byakuren's original temple.

However, the mystery of the UFOs hasn't yet been solved. Marisa discovers that upon opening one of them, a snake comes out and the UFO turns into a piece of wood. The girls take off once again into the night sky to figure out what's going on. Kogasa reappears in the process, again attempting to surprise the player. After that, the strange flying object appears again and transforms into a youkai named Nue Houjuu, who was the one that disguised the fragments. Apparently the player was the only one who saw the UFOs as UFOs - the enemies the player fought against knew that they were actually pieces of the ship. After defeating her, she explains that she was originally just trying to mess with Murasa's efforts to revive Byakuren, but the player caught her interest, so she ended up helping the player out too.