A character archetype that frequently appears in The Hero's Journey, the Mystical Waif is usually a physically young girl (although she may be Really 700 Years Old) with a plot-significant power. While most commonly female, a Mystical Waif could be a young boy, as long as he evokes feeling of protectiveness.
Ofttimes, she's a part of some mysterious, previously unknown society or race that possesses great magic, and she's not uncommonly the last of her kind. The bad guys usually want to exploit her powers to control/destroy the world, while the heroes want to save her out of chivalry or general contrariness.
Typically introduced as a part of the Call to Adventure, the Mystical Waif often appears to the hero seeking for his help while providing him with an exposition to the unknown aspects of their universe. Her introduction is what usually propels the plot from random adventuring to serious world-saving, as she recruits the rest of the party to help her collect the crystals, and she may spend some time as a Damsel in Distress before eventually joining the Heroes' team. If the story includes romance, she may eventually develop to be the Hero's Love Interest, or at least a contender for one.
Personality-wise, the Mystical Waif is usually pure-hearted and kind, although she may seem a little distant at times. She is also extremely naive about the world, and unfamiliar with even the most basic facets of the characters' lives — that is, she has No Social Skills, which can be Played for Laughs in the more light-hearted parts. She might not even speak the same language as the main characters' during her initial introduction to further highlight her cryptic nature. She can be selfless to the point of self-sacrifice at times.
Sure signs you're dealing with a Mystical Waif are odd hair colors; weird (by the standards of the game world), often futuristic-themed clothing; magical powers; blank, serious facial expressions; lots of ellipses in her speech; and an inordinate amount of attention from the villains. Frequently overlaps with Mysterious Waif, especially if her past or identity is kept hidden for most of the story.
She is a stereotypical party member in many RPGs. Gameplay-wise, the Mystical Waif is almost always magic-oriented, usually doubling as a White Magician Girl, or if more proactive, as Barrier Warrior or Squishy Wizard. She'll have weak physical stats, but strong magical stats and average-or-better speed. Her quality as a game character is almost entirely tied up in how powerful her attack spells are and whether anyone else has the ability to heal.
See also Mysterious Waif, Waif Prophet, Oracular Urchin, Barrier Maiden, Apocalypse Maiden and Mysterious Waif-tan.
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Anime & Manga
Hotaru Tomoe/Sailor Saturn from Sailor Moon seems to have many characteristics of this trope. She is mysterious, ready for a self-sacrifice, and wears unusually dark clothes; she also has several mysterious powers even outside of her Sailor Senshi identity (although many of the other girls did too). Her situation is somewhat different, as there are three sides involved: Sailor Moon, who wants to save her; the Guardians of the Outer Solar System, who want to get rid of her as she poses a threat to the world; and the evil Death Busters, who want to destroy the world with her help. A couple seasons later, she joins the main cast, and her powers overlap somewhat with those of the White Magician GirlCool Big Sis, Sailor Pluto.
Yagami Hikari from Digimon Adventure and Digimon Adventure 02, the human lightbulb. Also an Ill Girl, she is the only one to have a Crest (Light) that doesn't refer to an innate virtue or trait. The powers of this Crest usually manifest themselves in weird ways, and she has been shown as both 1) unusually self-sacrificing and 2) drawn to the Dark Ocean, because of her powers and walled-in emotional problems. She's also empathetic to the point of being borderline psychic, which sends her into two Heroic BSODs in 02 (and during the last one, her best friend Miyako has to literally bitchslap her back to sanity).
Reverie "Ren" Metherlence of Elemental Gelade is a mysterious and legendary weapon who is frequently rendered helpless and constantly protected by the main character.
Kisara of Yu-Gi-Oh!, the white-haired and blue-eyed Egyptian and homeless, quiet, vaguely psychic, mysterious keeper of the spirit of the Blue-Eyes White Dragon who sacrificed herself to protect the only person who ever showed her kindness, High Priest Seto...
Yukina from YuYu Hakusho appears young but, like her brother Hiei, is a demon and therefore may be much older than she appears. She is pure-hearted, kind, distant, naïve, and has blue (or, arguably, sea-green) hair. She is targeted by villains either for her gem-making powers (They come from her tears! Awwww!) or because the main characters care about her and she is no Action Girl. She occasionally serves as the group's healer, due to her abilities in that field.
Lala Ru from Now and Then, Here and There, who possesses the power to control water using a pendant that contains a vast reservoir of water. However, unlike most examples, she is neither pure-hearted nor kind. In fact, she hates all of humanity due to the utter HELL they put her through, and refuses to save the planet even though she has the power to do so. Until later, of course... but even then, you wish she hadn't.
One of the very first Star Trek fan clubs, "Spock's Scribes", published a journal with satirical fan fiction about young women passengers on the Enterprise who cause trouble. Spock's human cousin Samantha Scott, written by the only adult member of the club, was definitely one of these. The daughter of Amanda's sister Amelia and a Dr. James Scott (no relation), both physicians on planet XX Larid, she was Raised by Natives after her parents died in an earthquake, and picked up Psychic Powers from them. She caused and attracted random chaos on the ship.
Films — Live-Action
Flute, in the Elenium trilogy by David Eddings, is a small girl who is revealed, slowly, to have greater magical powers than anyone else in the party. She can control time and animals, among other things. Eventually they find out that Flute is actually the goddess Aphrael, which explains everything.
Luna Lovegood in Harry Potter Last of her line. Mother died when she was 9. Orphan's plot trinket = Butterbeer cork necklace and Dirigible plum earrings. Also pure-hearted and kind, distracted at times, weird, persecuted, absolutely adorable! Don't forget that she turns out to be pretty darned good at magic herself and can notice things that others don't.
House of Many Ways features a little white dog who is actually named Waif, who had been living with Charmain's great-uncle William (Wizard Norland) for a short time. Waif is no ordinary dog, but a rare, magical enchanting dog. Later, we find out that Waif actually is the latest generation of the Elf Gift, which (or, as it turns out, who) is supposed to protect the royal family of High Norland. However, unlike most examples, besides having magical powers Waif does not act very mystical, but like an ordinary dog, who begs for scraps, overindulges on human food, and clings to Charmain who she has adopted as her owner.
The Dresden Files: Through a horrifying series of events, the mantle of The Archive, the repository of all knowledge, was set upon a young girl. She can give a showing for herself in magical brawls set up as a trap for her personally.
In Terry Pratchett's Discworld novel Monstrous Regiment, Wazzer Goom fits this trope, as the brutalised girl who becomes the spiritual channel for communications with the long-dead Duchess of Borogravia.
Maia, the child with the ability of Precognition from The 4400 fits many of the characteristics of this trope, with her slightly creepy otherworldliness (and, of course, her potentially important ability).
Visas Marr from Star Wars: Knights of the Old Republic 2, though older than the archetype, otherwise fits this: she is sole survivor of the destruction of her planet, her species (Miraluka) are blind normally but "see" using the Force, and she speaks in strange ways. She can be sacrificed, if the player chooses to do so.
Isabella/Catleia from Advance Wars: Days of Ruin., though being from a strategy game she obviously doesn't have the RPG stats part of the trope, being instead a decent all-round CO with a Game Breaker CO power.
Mega Man Legends 2 has Sera, who plays the part perfectly, until after you collect the keys, when she takes over the ship and reveals herself to be the villain of the game.
Alouette from La Pucelle Tactics hits enough of the required traits to fit here. Although not the last of her kind, she is found with amnesia, is mostly good with magic (although, as with all Nippon Ichi games, you can customize her as you like), is self-sacrificing and is the current Maiden of Light, even if she doesn't know it, which is a powerful position held only by one woman at a time and chosen directly by the Goddess.
Avril from Wild ARMs 5 hits almost every single criteria for this trope. Silver hair, serious expression, unfamiliarity with customs, amnesia, sought by the antagonists, good with magic (although this is customizable), and Really 700 Years Old.
Lufia herself (and her analogues in the other games). She is kinda out-of-place in human society because she's actually a Sinistral, and the other Sinistrals want her to help them stay alive and do evil things, of course. She is also portrayed as cute, innocent, and a love interest of the hero, and of course, has lesser physical stats but uses magic well.
Subverted in Phantasy Star III with Maia, who is a mysterious, solemn, white-haired maiden who washes up on the beach, has no recollection of her past, and gets abducted by a dragon on her and Rhys' wedding day. Turns out the dragon is her shapeshifted brother, her amnesia was entirely mundane, and there's nothing unusual about Maia herself except that, of course, she's a princess. She doesn't even use magic.
Shana from The Legend of Dragoon reeks of this trope. First she gets kidnapped and put in jail, then she turns out to be the moon child who will destroy the world. She exhibits the personality traits of this trope down to the letter.
Kingdom of Loathing parodies this with the Quiet Healer, who often drops the Amulet of Plot Significance.
Rosalina, at least in Super Mario Galaxy, with her tragic backstory and enigmatic nature. Her other appearances eventually avert this, revealing she's quite a bit more resilient and playful than most examples.
Kanna from Three The Hard Way, the Really 700 Years Old alchemist, who is mysterious, secretive, and enigmatic in personality, and seems to know the Big Bad quite well. Gameplay-wise, she's a unique character with a relatively low physical and magical abilities, but can create and have access to alchemical weapons that can easily decimate Bosses. Despite being relatively useless in normal battles, one of the strongest party member actually remarks that they don't stand a chance against the Big Bad without her.
Melissa in "Fortissima's Treasure Hunters". She was apparently encased in a large green crystal for several generations, is able to shoot fire from her fingers, speaks a backward language (literally! The words in her speech balloons are spelled in reverse), and her eyes glow when she sleeps. I'll wager that there's plenty more we haven't learned about her yet...