Big Bad: Queen Chrysalis. Though she never actually attacks Fluttershy. Her threat is more to Fluttershy's identity and personal freedom.
Boisterous Bruiser: Rainbow Dash. Unfortunately for Fluttershy, as she really needed to talk to a Guile Hero, such as Rarity; or Science Hero, such as Twilight Sparkle. Alas, Fluttershy chose to open to her oldest friend, who has all the guile and mystical knowledge of a lightning bolt.
Fluttershy's mother is in fact crazy. She also believes that there are insect-like creatures who can take Pony form and that one of them sired Fluttershy on her. She is absolutely correct in both assertions.
Fluttershy herself makes seemingly-insane claims. Even her best friend Rainbow Dash doesn't believe them. Thing is, she knows one thing which means that her story of barely escaping the Changelings, and by implication of being half-Changeling herself, is probably true. She knows the name "Chrysalis".
Comically Missing the Point: Rainbow Dash, when she attempts "friendship" psychotherapy to cure Fluttershy of the "delusion" that she is of half-monstrous origin. She totally misses that Fluttershy lies to her the morning after her revelations, because 'Shy now assumes that RD won't believe anything she says about being part-Changeling.
Cosmic Horror: Fluttershy's origin is similar to that of the narrator from The Shadow Over Innsmouth. Indeed, given the subsequent events of A Canterlot Wedding, the most menacing part of that story also logically applies to this one as well, though Fluttershy never considers the possibility.
Daylight Horror: Adolescent Fluttershy encounters the Changelings by broad daylight.
Eldritch Location: Hive Chrysalis, located in a tunnel-riddled mesa near a menhir-crowned hill deep in the Palomino Desert. The hill is a good place to contact Changelings, and it is hinted that they keep watch on the hill for just this reason. Here's a description of the place:
Surely not the menhir-crowned hill, surely not the cave-riddled mesa, leering out over the landscape like a maggot-eaten corpse. There was a strange sense of unreality in Fluttershy's mind as she landed on the hill, as if she had left the sane normality of Cloudsdale and Ponyville, indeed of all Equestria, behind her, and entered some nightmare realm in which the fantasies of delirium were as one with the realities of the sunlit day.
The dry earth crunched under her feet. The desert wind whispered lonely through the time-eaten stones. Had they really stood here, been waiting here already when Equestria was founded, when the Pegasi migrated under the leadership of her illustrious ancestor, waited grinning and forlorn here back when the Cataclysm shook the Earth and the Age of Wonders vanished forever? Could they have been many millennia old, even then? Surely, nothing reared by Pony hooves was that old, was it?
Half-Changeling Fluttershy, who has the emotional powers of her father's kind.
Equinoid Abominations: The Changelings, in their true form. Fluttershy fears this about herself, but the indications are that the beautiful pink-haired canary-coated mare is her true form.
The Fair Folk: Fluttershy's mother goes seeking Flutter-ponies. She findsChangelings.
Fate Worse than Death: It is strongly implied that if Fluttershy had been captured by the Changelings, or even listened to Queen Chrysalis for much longer, she would have become the Queen's eternal thrall, serving her against Equestria.
God Save Us from the Queen!: Chrysalis. Fluttershy only ever hears her, and is nearly enthralled by her voice alone. But then, Fluttershy's father came from that Hive, and obedience to Chrysalis is embedded in her soul.
Heroic Bastard: Fluttershy was not sired by her mother's husband. She is still however descended from Commander Hurricane, as she traces that matrilineally. Her illegitimate origin has casued her grief because her father suspected this and rejected her, but then she doesn't really like her father all that much anyway. The part that really worries her is that she's pretty sure her real father is a Changeling.
Heroic Resolve: Fluttershy's will to live free is strong enough to enable her to overcome the genetic dominance of Queen Chrysalis and make a desperate — and successful — flight for freedom.
Gothic Horror: Fluttershy comes from a very old and messed-up family, check. her past hides a Dark Secret, check. Smells like Gothic Horror to me ...
I Am What I Am: By the time she tries to tell Rainbow Dash, Fluttershy has pretty much accepted that she is a Changeling-Pony hybrid. She still, quite rationally, fears Queen Chrysalis and other Changelings, but she is neither terrified of their mere existence nor does she assume that she is herself a monster in any but the most technical sense of the world. She is Fluttershy, and Fluttershy is free.
Word of God in comments to Bad Horse that the events of "Fluttershy's Night Out" are part of Jordan179's Fluttershy backstory as a teenager she was cruelly seduced, used and abandoned by a callous stallion which further explains why she's so terribly shy and afraid to seek a stallion. (This also makes Fluttershy's critical attitude toward her mother's actions somewhat hypocritical, while adding emphasis to why this disturbs her so much: Fluttershy is actually also criticizing herself).
"Sexual Orientation and Behavior of the Mane Six, In Context" makes it likely that Fluttershy's Two Mare Romantic Friendship with Rainbow Dash is somewhat sexual at least on Fluttershy's part, largely because Fluttershy may be bisexual (a Changeling tendency) and even more afraid of stallions than she is of mares. It also makes plain that Rainbow Dash may reciprocate but be too afraid of showing softer emotions to act upon it. Crippling shyness and emotional obliviousness are not the best combination for romantic happiness!
denies her descent even from her mother Sweetwing (and must be lying, given known Pony biology),
uses this excuse to rob her of the title of "High Lady" which she holds by right as a direct matrilineal descent of Commander Hurricane the First,
despises her because of her poor flight skills, presumed cowardice, and very un-Pegasus-like interests,
has learned about her encounter with "Nosey" and is willing to accuse her of prostitution based upon this, and
is willing to malign her friends (specifically, Rainbow Dash and Rarity) in support of his spurious accusations.
"Why I Cannot Believe in a Free-Love Equestria" puts Fluttershy's criticism of her mother's behavior and the events of Bad Horse's "Fluttershy's Night Out" in context: Jordan179 plainly believes that Equestria is a somewhat sexually-conservative society by modern Western standards, which means that Fluttershy sees casual sex as sleazy. This makes the events of "Fluttershy's Night Out" even more painful for Fluttershy within this continuity. Poor Fluttershy.
"Intercepted Mail: A Letter To Windvane" introduces Fluttershy's cousin Ill Wind, and strongly implies that he is the Pony who becomes "Dr. Atmosphere." It also strongly implies that Windvane is approaching the Moral Event Horizon of commissioning the Pegasus Device and engaging in mass equine sacrifice in order to power his treasonous plans to overthrow Princess Celestia and restore the Pegasus Mandate as a fascist dictatorship dominating all Equestria. In other words, Fluttershy is basically related (by her mother's marriage) to the in-universe equivalents of Hitler and Mengele. Poor Fluttershy.
Mood Whiplash: Starts as a beautiful idyll with two friends (Rainbow Dash and Fluttershy) enjoying Nature and each other's company. Takes a detour into Psychological Horror as we find that Fluttershy's mother is insane and Fluttershy's own sanity is shaky. Then goes into full-blown Cosmic Horror as we learn that Fluttershy ''really was'' sired by a monster. Finally, gets right back to a beautiful idyll as Fluttershy wakes up, seemingly all right, and the two friends enjoy a moment of pure ecstasy as they see the butterfly migration. Though Fluttershy's last words remind the reader that her half-Changeling nature is all still too real.
Mysterious Parent: Fluttershy knows that she was sired by a Changeling of Hive Chrysalis. She does not know which Changeling. Or why Changelings want to sire foals on Ponies in the first place. This is very obviously an other horseshoe waiting to be dropped.
Nature Lover: Fluttershy, of course. Even the knowledge that there are Changelings out in the Palomino Desert doesn't ruin it for her. Surprisingly, Rainbow Dash is also far from immune to Nature's charms. Just don't tell anyone she got all mushy about it ...
Non-Equine Lover Reveal: What happens to Fluttershy's mother, when she wakes up just a bit too soon and discovers she's lain with a Changeling.
Not So Extinct: Possibly, the Flutter Ponies, if they are from whence the Changelings came.
Pun-Based Title: The chapters are named after the four main stages in the life cycle of a butterfly. The third chapter is "Chrysalis." Which is also the name of the story's Big Bad.
Remittance Mare: Fluttershy. She comes of the oldest Pegasus lineage, her family is ashamed of her, she lives apart from them, and she never seems short of money.
Romantic Two-Mare Friendship: Fluttershy and Rainbow Dash. There's no hint that either of them want to act on any sexual attraction, but Fluttershy trusts Rainbow Dash enough to tell her a rather serious secret, and Rainbow Dash finds Fluttershy's beauty breathtaking when the normally shy mare is ecstatic about the butterfly migration.
As a half-Changeling Emotion Eater, Fluttershy can actually drain life force from those who feel positive affect toward her. For the obvious reasons, she tries to use this ability as sparingly as possible.
When the Shadow is prowling around Rainbow Dash's sleeping mind, the scent of Fluttershy lying down next to her causes Rainbow Dash to feel positive affect, which drives off the Shadow.
Fluttershy's mother was implied to be crazy before, but she goes madder after she mates with a Changeling and has Fluttershy, her half-Changeling daughter. Eventually, she is institutionalized.
Fluttershy herself almost goes completely insane when she hears the inhuman voices of the Changelings in their true forms and, what is worse realizes that she understands them, because she is one of them herself
Shrinking Violet: Fluttershy. The reason she chooses to have her conversation with Rainbow Dash, of all ponies, is that Rainbow Dash is one of the few ponies in the world with whom she's not that shy (because they're foalhood friends).
You Have to Believe Me: Fluttershy makes the mistake of telling her foalhood friend Rainbow Dash that Fluttershy herself was sired by a Changeling by introducing it as the ravings of her paranoid mother. Given that Fluttershy does not in any way look like the mythical flying creature the Pegasi know as "buzzies" and generally take about as seriously as we do UFO sightings, Rainbow Dash simply assumes that Fluttershy has gone a bit crazy under the stress of being the unfavorite member of a dysfunctional family. At this point, Fluttershy gives up trying to tell Rainbow Dash the truth. Justified, as in canon Fluttershy is normally a ''very'' poor communicator.