This section will only contain the portions of the story relevant to Mystina. It also focuses on the A ending (as does the rest of this site). For the full story, I recommend you play the game.
We first see Mystina in the halls of Flenceburg Academy, at night. She approaches a student, who informs her of Headmistress Lorenta's death. Upon returning to her room, she expresses relief at this turn of events, apparently done by one Lezard Valeth. Mystina enters a device, and we next see her in spirit form. She explores the Tower of Lezard Valeth, finding runes thought lost forever, and happens across his remaining homunculus. Mystina turns it into a crystal and takes it with her.
Back in Mystina's room, Lezard teleports in. Lezard tells Mystina he's obtained the Philosopher's Stone and politely asks for his homunculus back, offering information in return. Mystina asks him for information on Bifrost, the rainbow bridge that connects Asgard and Midgard. Lezard informs her it is in the forest of the World Tree, where the elves reside. Mystina says the elves piss her off and wishes they'd all curl up and die, but Lezard remarks that would be quite bad. The elves protect Yggdrasil, the World Tree, and without it the world would wither and die.
Lezard then tells Mystina he made an interesting discovery while developing his homunculi. The gods require elves to walk upon Midgard, making them vessels of the gods and, in a manner of speaking, gods themselves. Furthermore, humans and elves can reproduce, making half-elves, and Odin himself is one. Odin ascended to the throne of the gods after the great war and created the second race of man. The question, then, is how exactly Odin got the power to do so, considering he started out a weak god. Lezard explains that humans are incomplete, and gods are the final, static evolution of man. But because Odin was a half-elf, he could grow, and thus grew in power and ascended to the throne.
Lezard goes on to explain that human souls can be transferred into elves, thus making it possible for humans to ascend to godhood. And his homunculi are essentially half-elves. Thus, if one was to shift one's soul into a homunculus, one would become a god.
Lezard leaves Mystina with that to consider, and we see her walking through Flenceburg in her spirit form. She hears Lezard's voice, and he tells her his plans are about more than godhood. Rather, he seeks the means to seal a divine soul in a homunculus. Lezard then warps into Mystina's lab and freezes the device she leaves her body in while in spirit form, killing her.
We see Lenneth and Mystina, and the valkyrie offers Mystina a place among her einherjar and offers her the chance to learn more about Bifrost and Yggdrasil. Mystina accepts, though she says she doesn't need stupid promises.
Lenneth goes to the Weeping Lily Valley and finds the other earring Lucian left there. The seal on her memories of her past life as a human is unlocked, but before anything can happen her sister Hrist awakens in the valkyrie's body. Arngrim and Mystina come running in, having heart Lenneth's call for them, and find Hrist. She demands they serve her, which both einherjar refuse outright, and tells them Lenneth has been deemed unfit for her task. Hrist decides if they won't obey her she'll simply dispose of them, but enough of Lenneth is left to protect them. Failing that, Hrist leaves.
Mystina hears a voice that tells her to crystallize the dissipating remnants of Lenneth's soul and does so. Lezard warps in, and Arngrim and Mystina realize their only hope to save Lenneth is to work together with him. Lezard tells Mystina to put Lenneth's soul in his homunculus, and though she knows it's playing straight into his plans, they have no other choice. Once it is done and she is stable for the time being, they go to the vampire Brahms's castle to retrieve Valkyrie's true vessel. Brahms helps them defeat Hrist, and once she's reduced to wisps Mystina crystallizes them. Mystina and Lezard restore Lenneth's soul to her vessel.
There's quite a bit more plot to the game, but the rest of it does not involve Mystina directly and thus has no bearing on this site.