Mare of Steel: The story that started the universe. After returning home from a meteor shower, Rainbow Dash finds a green rock that makes her violently ill when she touches it. Later, she begins a journey to discover just who she is and what her place in Equestria is, becoming the hero Supermare. Complete.
Mare of Steel also has a collection of side stories dealing with smaller adventures and encounters that would otherwise slow the main story down.
In Brightest Day, In Blackest Night When a mysterious ring finds it's way into the Crystal Empire, Shining Armor is introduced to a universe far beyond anything he could have imagined. As he works to master new skills and powers, he stumbles upon a threat that could spell doom for him, his home and family, and thousands of other beings across the galaxy. In Progress.
In the sense that Rainbow Dash has superpowers and General Zod has been impersonating Prince Blueblood for years.
Since Mare of Steel was first published before Season 3 aired: Rainbow's mother Firefly is head coach of the Wonderbolts, and her father Thunderhead does not match the description of the pony seen in Games Ponies Play.
Twilight's note that overloading magic could cause a pony to explode.
Deathstroke's sword, which is capable of cutting even Supermare. She breaks it, but Silversmith retrieves the pieces, which have blood samples on them he can experiment on.
Cloning Blues: In one of the side stories, Rainbow Dash is hit with a spell that not only drains her powers, but creates two duplicates of herself based off her intelligence and strength (colored Blue and Red respectively). She ends up regaining her powers and destroying the clones by the end of the story.
Freak Out: Rainbow does not take the news that she's really a Kryptonian well. She gets better eventually.
General Ripper: Steel Wing is willing to do anything if it will stop Supermare.
Gilligan Cut: One is used to highlight how pointless Steel Wing's paranoia over Supermare is; his first scene ends with him ranting how she's probably "in her secret lair, plotting (Celestia's) downfall", at which point the scene switches to Rainbow Dash waking up from a nap in one of Applejack's trees.
Harmless Freezing: Rainbow Dash does not really have good control over her freeze-breath when sneezing, and ends up freezing a butterfly when it lands on her nose, and Fluttershy when she brings the butterfly to her. Both are unharmed by the end.
She uses this to defeat Clayface in the side story "The Kryptonian and the Bat", drenching him in water before freezing him solid.
Happily Adopted: From what we can see, Rainbow was very happy with Firefly and Thunderhead. She still keeps good connections with Firefly even after she learns they lied to her about being an alien.
Heel-Face Turn: Happens off-screen for Trixie, being as Act II takes place after the episode "Magic Duel".
I Have Your Wife: Brainiac kidnaps Scootaloo to use as leverage against Supermare.
I Just Want to Be Normal: Rainbow Dash freaks out and has this reaction when she learns she's really a Kryptonian. She grows out of it eventually.
Insane Troll Logic: Rainbow's rationale for why the Kryptonite that poisoned her is evil: Various villains they encountered used green magic. The Kryptonite glows green. Therefore, the Kryptonite is evil. Twilight lampshades this.
It's All My Fault: A side story set after the conclusion of the main story shows that Rainbow Dash blames herself for her mother almost getting killed by Brainiac, at least until Firefly convinces her it isn't.
It's Not You, It's My Enemies: Rainbow Dash tries to use this on Thunderlane after Brainiac threatens those close to her, but he refuses to let her go.
It's Personal: Somehow both Zod and Brainiac manage to achieve this by their own designs. Brainiac gets especially personal when he injures Firefly.
Kirk Summation: When Rainbow Dash first runs into Trixie in Seaddle, Trixie tries to say they're Not So Different by pointing out that they're both braggarts. Rainbow shoots her down by pointing out that at least she knows to stop before someone gets hurt, and then when Trixie tries to challenge her to prove who's superior, Rainbow just walks away, saying she's not worth it. Trixie has a brief Villainous Breakdown at this.
A month before the start of the story, Twilight, Pinkie, and Applejack went camping, and Pinkie ended up accidentally burning one of Twilight's books, causing her to have a Freak Out that outshined the one she had in "Lesson Zero". AJ and Pinkie calmed her down, but both swore they'd never go camping with her again.
Celestia and Luna both refer to earlier encounters with Kryptonians, with Luna saying that she owes them a "great debt".
Rainbow Dash get a moment like this when trying to break through Brainiac's Force Field in Chapter 23, after Brainiac says that she must comply with his plan:
Rainbow Dash: No... I... won't! (breaks through to save Scootaloo)
Red Oni, Blue Oni: Red Dash and Blue Dash; one is based off of Rainbow's physical and emotional prowess, while the other is based off her intelligence and logic. Rainbow gives each of them a "The Reason You Suck" Speech before beating them.
Retcon: Originally, Soarin' was supposed to be Rainbow's love interest, but this was changed to Thunderlane and Soarin' was made Diana's love interest.
It underwent another, changing Rainbow's Kryptonian name from Kara Zor-El to Kara Jor-El (to better match with Kryptonian naming styles)
The Reveal: General Zod has been posing as Prince Blueblood for the last five years.
Sadistic Choice: Brainiac offers Rainbow one: if she saves Scootaloo, a bomb planted in Cloudsdale will detonate and kill everyone, but if she goes and saves Cloudsdale, a power surge will kill Scootaloo. Rainbow Takes a Third Option and decides to save them both.
Sealed Evil in a Can: At the end of the story, Brainiac is petrified by the Elements of Harmony, and Rainbow Dash puts him in storage in the Fortress of Solitude for safe keeping.
Celestia, the Mane Six, and Firefly become this for Rainbow Dash.
Thunderlane figures out who she is during her fight with Brainiac.
She and Batpony become this for each other in one of the side stories, when he deduces her identity, and she uses her X-Ray Vision to see that he's really the real Prince Blueblood.
Sequel Hook: It ends with two. First, there's the fact that Silversmith is still free, and has samples of Supermare's DNA to experiment on. More importantly, the last scene shows Darkseid opening a boomtube to Equestria, setting the stage for the main Justice League of Equestria story.
(blocks blow) "Iíll only kneel to two ponies. And youíre not one of them!" (throws Zod through a wall)
In the second arc, there's her refusal to submit to Brainiac's Sadistic Choice and letting him break her, instead saving Scootaloo and rushing off to stop the bomb in Cloudsdale.
"Welcome to Equestria, Brainiac."
Smug Smiler: Silversmith. Rainbow Dash is disturbed by it.
Sneeze of Doom: In one of the side stories, Rainbow Dash's super-breath causes her to freeze a butterfly that had refused to shift from her nose, and then Fluttershy after she takes the butterfly to her. Both are unharmed by the end. The first sneeze also strips several apple trees of apples and leaves.
Stealth Hi/Bye: Batpony (the local Batmanexpy) does this several times to Rainbow Dash in their multipart side story crossover.
Strawman Has a Point: In-universe; during her interrogation, Rainbow admits that she would be a big threat if she ever went rogue, and even admits that some things that Silversmith was saying seemed true enough (on the surface)
Superdickery: Discussed; After becoming Supermare, Rainbow begins to contemplate if performing pranks while dressed up as Supermare is a bad thing. Trixie returns and threatens to destroy Ponyville with an Ursa Major before Rainbow can make up her mind.
Take That: The entire Red and Blue clone side story is one to the Superman: Red & Blue storyline.
Taking You with Me: In the final battle of the first arc, Zod overloads his magic in an attempt to blow up both Rainbow Dash and Canterlot. Rainbow flies him into the upper atmosphere before that happens, but she is badly injured in the blast.
Thou Shall Not Kill: Rainbow Dash, just like canonical Superman. She get very close to breaking that rule when Brainiac seemingly kills Firefly.
"Would your mother have wanted this, Rainbow Dash?"
What Could Have Been: Word of God is that originally, there wasn't going to be a whole series of stories, but rather just this one. It would have continued past the second arc to Rainbow Dash and the other Mane Six fighting off Darkseid, with the fallout causing Rainbow Dash to go into self-imposed exile. Then there would have been a Time Skip, followed by adaptations of Superman Returns, "Superman vs. the Elite", and The Death of Superman before finally finishing. However, the author was inspired to write a whole series of crossovers, so those plans were scrapped.
Why Don't You Just Shoot Him?: After defeating her in their first fight, Zod lets Rainbow Dash live (albeit slowly being killed by a Kryptonite necklace) so that she can watch his Evil Plan to assassinate Celestia succeed. After she escapes and prevents this, he admits it was a mistake and decides to kill her.
Xanatos Gambit: Zod sends the Flim-Flam brothers to attack Ponyville in order to "test the waters" — if they succeeded, he would have had an unstoppable weapon at his disposal, and if they failed, he'd get a look at what he's up against.
Xanatos Speed Chess: Brainiac is constantly updating and modifying his plan, especially when he deems Steel Wing more trouble than he's worth and choosing to ally with Silversmith instead.
Boring but Practical: Diana takes a coil of rope into the first test during the tournament (at Athena's suggestion).
Butt Monkey: Soarin' is at the mercy of an island's worth of Amazons that might kill him at the slightest provocation, not to mention Athena messing around in his head.
Calling The Old Mare Out: Diana does a less severe version to Hippolyta, calling her out for putting her own personal preferences before the will of the gods.
Can't Get Away with Nuthin' : In chapter 2, Diana is participating in a dare to steal eggs from a phoenix nest. She hesitates, and the phoenixes chase her away and she gets several "I told you so"s from the other Amazons.
The Cameo: Rainbow Dash as Supermare makes a brief appearance during Diana's flight in Chapter 6.
Culture Clash: Diana's upbrining as an Amazon does not mix well with Equestria's more open social norms.
Cutting the Knot: Diana does this literally during the second test of the tournament.
Did You Just Flip Off Cthulhu?: During the Nightmare Moon Incident, Diana pounces on Nightmare Moon when she tries to kill Hippolyta. At the time, Diana is less than one year old.
Does Not Like Colts: Most Amazons, but especially Phillipus; she tries to kill Soarin' on sight when Diana brings him into Themyscira, and tends to act more aggressive when there is even the slightest mention of the mortal realm.
Everybody Hates Hades: Subverted. Hades shows up, but outright refuses to aid Ares in his plans, not even when offered a way to ensure he gets plenty of souls for his domain (stating that everyone ends up there eventually anyway). In fact, the only way Ares gets any support from Tartarus is that Persephone tells him about the Alicorn Amulet's abilities, because she somehow thinks she's helping her husband out.
How We Got Here: The story opens with Soarin' waking up on Themyscira and being confronted by Diana, with the next couple of chapters being spent showing her backstory and how he ended up there.
Mythology Gag: Diana's backstory is the old "made of clay" backstory, with the Elements of Harmony rather than the gods bringing her to life.
Much of the story is based on the 2009 animated Wonder Woman movie. Or rather, the tvtropes page for it, as the author admits to not having seen it yet.
Nice to the Waiter: Hades insists Ares pay the toll for crossing the River Styx even if its not necessary for gods, because Charon works too hard to be ignored.
Noodle Incident: Apparently, Cadence broke each of her legs at various points while being raised by the Amazons. But Diana had it worse.
Weaksauce Weakness: Yellow, for the Green Lantern rings. Shining seems to be the only one who's noted how odd this is.
Why Did It Have to Be Snakes?: Shining Armor is implied to have developed a fear of Changelings due to his experience with Chrysalis. Since Green Lanterns are explicitly chosen for their ability to "overcome great fear", this will be plot-relevant.