Lotus Land Story/Story
This article details the story of Lotus Land Story.
All is well within Gensokyo, and just as the shrine maiden Reimu Hakurei is beginning to grow bored, a massive amount of youkai appear and begin to lay waste to the Hakurei Shrine. Although Reimu immediately sets about exterminating the invaders, she isn't able to compete against the sheer numbers of youkai. She determines that the creatures are emanating from a suspicious lake high in the mountains behind the shrine, and sets out in an attempt to staunch the flow and save the shrine from complete destruction. Around the same time, Marisa Kirisame, a powerful magician, senses a great energy lurking beneath the mountain lake and hurries toward it herself, fully intent on making the mysterious power her own. The two of them set out separately to go there.
Both characters easily plow through Orange, an ordinary youkai who was simply flying about the mountains, before arriving at a blood-filled lake, which was their destination. There, they encounter a vampire named Kurumi, who claims to be the guardian of the lake, and battles her twice. After defeating her, they discover a vast chasm in an island at the center of the lake from which the mysterious power emanates. At the end of this passageway stands a dark mansion called Mugenkan. Outside they find the scythe-wielding gatekeeper Elly, who explains that they are within the boundary between the real world and the Fantasy World. She also reluctantly admits that the other character (Marisa, if you're playing as Reimu, or vice versa) has already defeated her and entered the mansion.
After braving the attacks of the mansion's housekeepers, who apparently aren't thrilled to have visitors, Reimu and Marisa finally meet in a dark chamber near to the center of the building. Reimu immediately accuses Marisa of planning something devious and demands that she leave, to which Marisa takes offense, and the two engage in an explosive duel. The victor demands that the other leave before continuing into the fantastic heart of Mugenkan. There the remaining protagonist accidentally awakens a sleepy youkai named Yuuka who, despite her weariness, wields tremendously powerful attacks. After her defeat, Yuuka panics, fleeing the area and forcing the heroine to give chase. In a star-filled fantasy world, the final battle begins.
Some time later, the characters are bored and somehow stumble into another strange world, in which they encounter tremendously fierce enemies and the twin sisters Mugetsu and Gengetsu. Although they battle, it is ultimately a pointless affair.
Note that no explanation or context for LLS' extra stage is given in any canon or semi-canon material. The extra stage of Lotus Land Story quite literally happens without any background; the stage begins with the player character starting in a dream world which isn't alluded to in anyway by the main scenario or any ending