Touhou - Mountain of Faith (Touhou 10)

Like all Shinto shrines, Gensokyo's decrepit Hakurei Shrine was originally created for the housing and worship of a patron god. However, because all sorts of youkai are known to hang about the shrine, the local humans have ceased to visit and their faith in the shrine's god is dwindling, diminishing its strength and influence. Reimu Hakurei and Marisa Kirisame begin an adventure to reach and ascend the mysterious Youkai Mountain with the hope of finding a solution to this problem.

Mountain of Faith features two playable characters, each with three weapon types (but no personalized Spell Card bombs). In a break from previous games, collecting power items results in an increase in "option" satellites around the character (for a total of four), which behave differently according to the character and weapon type. Each characters' options also fire bullets, and either shift position or freeze in place in focus fire mode.
The scoring system is based on the Faith meter, which has a refillable gauge and a numeric value (minimum 50,000). As long as the gauge is partially full, the player's Faith value doesn't decrease, but the gauge is always emptying unless the player is killing enemies or collecting point items. Point items also partially refill the gauge, and Faith items increase the numeric Faith value. The Faith value directly affects the point value of point items and Spell Card bonuses.

Story:

Autumn has come to Gensokyo, and to its only shrine, the Hakurei Shrine, a common meeting place for its youkai that was seldom visited by its humans. As a result, faith in the Hakurei Shrine's deity began to fall like the leaves from the trees. It's in such a season that Reimu Hakurei, the shrine maiden of the Hakurei shrine, is visited by a mysterious stranger who claims to represent a god of mountains and orders her to shut the shrine's doors for good. Reimu is deeply troubled by this state of affairs, as she knows the shrine can't be allowed to close down due to the role it plays in watching over the Great Hakurei Border. Marisa Kirisame, her ordinary magician friend, is suspicious and also suitably bored. Depending on who you choose, one of these girls finally decides to ascend the Youkai Mountain to confront the mysterious deity behind the threats.
En route to the mountain, the heroine encounters several of Gensokyo's myriad gods, including two spirits of autumn, Shizuha Aki and Minoriko Aki, and a curse god, Hina Kagiyama, who tries to chase her away from the dangers of the mountain (unsuccessfully). As our heroine reaches the foot of the mountain and begins to climb it, another youkai appears to try to convince her to leave - Nitori Kawashiro, the valley kappa. After Nitori's equally unsuccessful bid to get her to go away, she mentions that a god has recently appeared on the mountain, causing some trouble for the tengu and kappa that live there.
Ascending the waterfall that fed the rivers Nitori swam in, the heroine faces the forces that guard the mountain from outside influence, including Momiji Inubashiri and the traditional tengu reporter, Aya Shameimaru, who was sent to investigate by the leaders of the tengu society due to her familiarity with outsiders. Aya puts up a token fight, but eventually allows the human interloper to pass on to the lake where a new shrine, the Moriya Shrine, has appeared. As she enters the grounds, she is confronted by a new shrine maiden - Sanae Kochiya. Sanae says that the lake and the Moriya Shrine were both recently moved to Gensokyo, and that she intends to collect all of Gensokyo's faith for "Lady Yasaka". Naturally, to do that would mean the end of the Hakurei Shrine, to which our heroine objects, leading to a battle where Sanae is ultimately defeated. At the top of the mountain, our heroine finds a lake surrounded by pillars, and Kanako Yasaka. Kanako, a goddess of the wind and rain, seeks to gain all of Gensokyo's faith in order to prevent the declining level of faith in Gensokyo to reach the point where its gods lose their power. Were such a thing to happen, she believes, Gensokyo would fall into a state of chaos. After a protracted battle, however, Kanako is convinced to make peace with the tengu and kappa, who are also convinced to accept her as the goddess of the Youkai Mountain.
Once the issue is resolved, Reimu resumes her normal life of cleaning and whiling away the time with Gensokyo's youkai, and Marisa turns to sneaking into the mountain for chestnuts. While pilfering snacks from a monstrous chestnut tree, it seems she'd heard a rumour that there was another god at the Moriya shrine. This, and the observation that Kanako had taken residence at the lake, and not at the shrine, the two set out for the mountain again. Kanako attempts to chase them off, but they eventually reach the inner sanctuary and discover Suwako Moriya, the shrine's true god, who tells them that Kanako defeated her in battle long ago, thereby winning use of the shrine in the public eye, though it was mostly left as Suwako's demesne - though it was by Kanako's hand that the Moriya shrine moved to Gensokyo. As our heroines make ready to leave, Suwako demands they play with her, just like they've played with Sanae and Kanako - with beautiful danmaku barrages.

Did you read all of that? Yeah, I doubt that, but it's actually the first Touhou storyline with any depth.
My favorite touhou game so far.