Undefined Fantastic Object/Story
This article describes the story of Undefined Fantastic Object in detail.
During the events of Subterranean Animism, the action taken by Kanako Yasaka and Suwako Moriya towards their "industrial revolution" project for the Youkai Mountain - giving Utsuho Reiuji the powers of the god Yatagarasu in order to invoke nuclear fusion deep underground - ends up causing geysers near the Hakurei Shrine to spring forth, bringing evil spirits with them.
The group of youkai consisting of Shou Toramaru, Nazrin, Minamitsu Murasa, Ichirin Kumoi, Unzan, and Nue Houjuu is shot above the surface into Gensokyo by these geysers after having been buried and sealed in the ground for over a thousand years. With them comes the Palanquin Ship, a flying vessel captained by Minamitsu. Shou, Minamitsu, and Ichirin then vow to rescue Byakuren Hijiri from her seal in Hokkai. Unfortunately, the fragments of the floating vault, one of the pieces necessary for Byakuren's revival, were scattered all over the place by a prank of Nue's, where she planted the seeds of unknown form into the pieces(the youkai didn't know what the others were planning, but thought it would be funny if they failed). In addition, Shou loses the pagoda of Bishamonten - the second piece necessary for unsealing the monk - and sends Nazrin to find it.
The story of Undefined Fantastic Object starts in earnest in early spring, after the snow begins to melt, with rumors around Gensokyo of a strange flying object in the skies. Believing the Palanquin Ship to be a treasure ship, Reimu Hakurei and Marisa Kirisame are prompted to chase after it. In turn, they are followed by Sanae Kochiya.
The heroine first runs into Nazrin, who is busy searching for the pagoda using her dowsing rods. Since the heroine has already collected some of the pieces of the floating vault (in the form of perceived UFOs), Nazrin decides that the heroine is worth the effort to fight. However, she ultimately loses, and manages to escape in the end, settling on finding just the pagoda. It is known that she finds it between now and stage 4 or 5 at a second-hand shop, which could be referring to Kourindou.
Still chasing the flying ship, the heroine then meets Kogasa Tatara, a youkai with no relevance to the story. After the youkai fails to scare the heroine, she is promptly defeated in a high-speed battle.
Once the heroine reaches the Palanquin Ship, she meets Ichirin and Unzan, who are standing guard outside the ship itself. Many fairies and youkai have been swarming around because of the rumors that there is treasure on board, but Ichirin assures the main character that this is not the case. The heroine beats the pair and enters the ship.
Inside the ship, the heroine has her first encounter with Nue, who is concealing her true form at the moment. After she retreats, the heroine meets the captain, Minamitsu, who reveals that the ship is currently on its way to Makai under autopilot. The main characters generally react poorly to this, though no further mention is made of the older Touhou games. Minamitsu attempts to battle the heroine, again in order to wrest the fragments of the floating vault away, but in the end she assumes that the heroine is on their side and is trying to help.
Once in Makai, the heroine disembarks, only to be overtaken by Nazrin once again. The mouse youkai has found the pagoda, and decides to test it out before giving it to her master, Shou. The heroine beats the two of them, and finally decides to break the seal on Hokkai out of pure curiosity.
After the seal is broken, Byakuren appears to the heroine. A friend to all youkai and humans, she and the main character have a battle of words, but one way or another, they end up fighting. Once the heroine wins, it is implied that everyone leaves Makai(and Byakuren is not sealed away again).
Bad Endings (Reimu)
She ends up getting caught and trying to figure out a way home with A being more mindful preparations to fight them while B has her finding the ship and wondering why it won't fly and concerned about leaving the shrine alone.
Bad Endings (Marisa)
Similar to Reimu, she's stuck in Makai, but A has her becoming bored due to how peaceful the youkai there were being while B has her trying to get home with all the treasure she found.
Bad Endings (Sanae)
She's stuck in Makai and A has her finding due to Byakuren's speeches that Youkai might not be so bad though she's still reluctant to put them on the same level as gods. She still wants to go home. B has her unbending in her ways but realizing she's in no place to do so as she surrounded by youkai.
Ending (Reimu A)
At the shrine, Reimu and Marisa are talking about the incident's details and how the Palanquin Ship is still flying. Reimu plans on investigating it. There she finds Byakuren and Minamitsu who talk about how nice it is to fly in Gensokyo. They then talk about where she lived and the problem with the ship flying, which Byakuren takes into consideration. It goes to state Reimu suggest making the ship a real treasure ship, which became successful as Byakuren notices the peace between youkai and humans in gensokyo. Reimu's confused by that as she doesn't know why she was sealed in the first place. It states that in Gensokyo Byakuren and her followers have nothing to fear as powerful humans aren't feared in Gensokyo.
Ending (Reimu B)
Byakuren visits Reimu at the shrine as she suggests Reimu do more than just hunt youkai, referring to the angry god of the shrine. They talk about where Byakuren lived with Reimu assuming she was from Makai as Byakuren replies she's from this world. Byakuren then announces her plans for a temple where she'd try to help Youkai (who are oppressed by the shrine maiden she adds). Reimu's not happy about having another rival or the remark made. It states that ship was turned into temple which became popular with both humans and youkai, much to Reimu's dismay.
Ending (Marisa A)
Marisa's at the shrine talking to Reimu about the incident and how well she got along with them despite fighting and the things she found in Makai. She goes on to say that she's able to go there and back when she likes, with Reimu being disinterested. It notes that Marisa asked Byakuren to allow such trips and Byakuren liking Marisa's personality allowed it as well as offering other assistance, which Marisa planned to take advantage of. Though the UFOs were still a mystery to her and Byakuren.
Ending (Marisa B)
Marisa's at home investigating a UFO which stopped flying as it soon opens up revealing a small snake toy which comes to life and as it leaves the UFO it becomes a block of wood and she figures out the relationship between the shape changing and the snake but it escapes too quickly for Marisa to do more. She decides to investigate this soon. (A direct tie in to the extra stage)
Ending (Sanae A)
At the Moriya shrine, Sanae tells Kanako about the incident as they see an ad Byakuren put about helping a temple. Sanae asks them to help with that as she made a deal to return home. Kanako's suspicious but decides to help, seeing it as a chance to see what Byakuren's really like. She also insists on Sanae helping despite her not being good at manual labor. Kanako notices how the youkai around her revere her as she talks with her. She notices her background isn't false, but she's even more cautious of Byakuren as a result noting she wasn't ordinary.
Ending (Sanae B)
Suwako and Sanae are at the ship talking with Byakuren with the main topic being the UFOs which Byakuren see only as pieces of wood as they have a disagreement on what they really were. Suwako noticed the mystery but in the end the two decided that storehouses were round back then.
After the events of the main story, Marisa decides to open up one of the UFOs. Much to her surprise, a snake comes out, and the UFO changes in appearance to be a simple piece of wood. She discusses this with Reimu and Sanae, and they discover that they were the only ones that actually saw the UFOs as such - everyone else saw them as wood, the actual fragments of the floating vault. They realize that something else has been going on behind the scenes, and decide to investigate.
Their investigation leads the heroine to Kogasa Tatara, and, eventually, Nue Houjuu. She reveals that she was the mastermind behind placing the Seeds of Unknown Form onto the pieces of the floating vault, and she and the heroine engage in a long battle. Afterwards, Reimu decides not to exterminate her, Marisa learns more about Nue herself, and Sanae decides to get their picture taken with Aya Shameimaru.
Byakuren, Shou, Minamitsu, Ichirin, Unzan, and Nazrin all fly around on the Palanquin Ship for a while, but eventually settle themselves near the Human Village and renovate the ship into a temple, which they name after Byakuren's younger brother. The temple becomes popular with youkai, and eventually Nue realizes that something like this would benefit her as well, and joins them in living there.