Um, I have an idea. Rainbow Dash reacts realistically after TMMDW episode, meaning that she flies off after punching Twilight in the face, winds up somewhere in Canterlot, where she runs into either this universe's version of Batman or the writer of the Batman comics. In either case, both are washed-out versions of their former selves and Rainbow is a huge fan. Hearing Rainbow's plight, he is inspired to train Rainbow, and he turns her onto being a real vigilante. His "I work alone," anti-friend/companionship shtick really gets to her, causing an even greater rift to form between her and her friends, causing her to question their integrity and her own element as she reviews their actions during the episode.
Her friends search for and do find her, but she's colder and more distant. She comes up with a legitimate excuse to stay in Canterlot, taking a promotion from the Weather Patrol she had turned down before to stay in Ponyville. Her friends send letters, but she becomes more embittered toward them and less and less involved, letting them clutter up her mailbox without reading them eventually.
Around this time, the mentor character (Batman as a pony or the writer of Batman), sees fit to test Dash by making her go out into Canterlot to fight crime as he once did/wrote about. Rainbow Dash, similarly to how Batman took the bat and made it his own, makes Mare-Do-Well her own, a personal symbol about betrayal and the failure of friendship. If you want to look into it, it's about her lost identity at this time. Rainbow Dash is a textbook cheesy hero, and the scenes here have a lot of potential for some fun parody and satire of the superhero genre in the tone of the show. She, of course, kicks some serious flank, and as she continues her work, she causes the Princesses, and the country, to take notice. This is particularly unfortunate given that her friends know of her and her situation. She rushes around to cities all across Equestria, discovering hints of a conspiracy in Canterlot. However, she's not exactly the world's greatest detective, and she is becoming more and more tired from having to do her work and keep up a secret identity. Her boss sends her to Ponyville to vacation, noticing the exhaustion, pulling out the letters as evidence that she had things to make right there. Knowing that she must keep up her training, the mentor character gives her a guide to being a superhero. Again, tons of room here for fun parody.
She returns, brushing off her friends and giving Applejack a piece of her mind when she follows. The other characters are baffled by her behavior and are even a bit rude to her because of it. Twilight tries to talk to her, but she just seems hurt and rushes off. (in this story, they're reading buddies who hang out a lot and are rather close). In this section of the story, Rainbow Dash tries to keep her identity a secret while her friends are trying to figure out what's wrong with her and why's she so mean all of a sudden, partially on behalf of the Princess Celestia herself. Dash also tries to figure out the big mystery around Canterlot, but is too tired and stressed to connect the dots. All of her friends, especially Twilight, try to talk to her and befriend her again, but she's conflicted between her friends and the advice her book gives her (which has more room for parody, by the way. She makes a secret lair and everything, with HORRIBLE names for everything). It isn't until Rainbow Dash confesses her reasons for being mad and hurt to Applejack and Applejack DEFENDS what they did that she has a breakdown and allows Twilight to talk to her. Twilight explains how it was all her fault and that she shouldn't blame anyone else, and the two begin to rekindle their friendship (in this story, they're reading buddies who hang out a lot and are rather close). She starts being friendly to Fluttershy and Pinkie again, but Rarity and Applejack are less than willing to accept their former friend (not that she was exactly extending the olive branch) to them, so they don't exactly all hang out. While she's okay with PP and FS, she mostly hangs with Twilight, hiding herself from the others, eventually staying with her instead of on some cloud or in her lair. This is the big conflict of the story: Rainbow Dash's identity crisis and the ties of it to her friends, and the AJ fight and the events afterwards are around where it starts building up to a fever pitch.
Twilight begins to figure out what's going on because Dash doesn't really stay until the morning, not to mention that she's begun to figure out that not all is quite right in Equestria. She figures out Dash's identity, and while there is some fear from Dash, she trusts Twilight, and after consulting her book (and hearing Twilight talk about tons of things she hadn't figured out yet), she invites her on as her sidekick, going by her book and Twilight's logic. Twilight isn't thrilled with vigilante...ism, but she's attached to Dash and want's to figure out what's going on, not to mention there has been some suspicious behavior from Celestia lately. She resolves to stay behind and research while Dash does the dirty work. A few days later, Twilight announces intentions to go with Rainbow Dash to Canterlot shortly after on "some business for the Princess" (in reality finding things out with Dash), and then marvelously chews out AJ (sorry, gal, I love you, but you need a character arc!). They decide to stay one last night, but it appears that they've dug too far, as they've attracted the attention of what appears to be the royal guard. They search for Dash and Mare-Do Well, not realizing that they are the same pony, and when they realize Twilight has gone missing, they assume that she's connected.
When they arrive in Canterlot, they find that the mentor character has been arrested in connection to the sightings of him with Mare-Do-Well, and there's a witch hunt for Dash, Mare-Do-Well, and Twilight, seemingly headed by Princess Celestia herself. Twilight still is uneasy with things, but she leaps into the action with Dash as they investigate the corruption further. (The scene where Twi goes out with Dash for the first time to fight crime is supposed to be a welcome break from all the darkgrim grimdark stuff. PURE comic gold.) Luna herself eventually signals for them using something similar to the Bat Signal, as she explains how Celestia isn't fond of vigilantes but how she (Luna) recognizes their progress and their ability to do more than the princesses could, AND how Celestia is being rather strange as of late. This is meant to show the growing divide between the princesses. I don't see them teaming up, unfortunately, but she becomes the Commissioner Gordon, of sorts, feeding them information. I really want there to be a "Rainbow Dash disappears while Luna is talking about both Twi and Luna are completely surprised" scene. It just must be. They grow closer as they work and develop a nice dynamic and build an extremely close friendship. This is also the point where Mare Do Well becomes a symbol against crime and a symbol of hope for the citizens who have become disenfranchised with the princesses because of the lack of action about the growing crime rate in Canterlot and the new goings on. And of course, a growing black and grey morality springs up because of their need to steal to eat and such.
After gathering a large piece of evidence after busting a hideout, Twilight is kidnapped. It's either during the raid or sometimes during the night when Twilight is at the hideout researching. No real preference. The point is that Dashie finds a note about Twi and the mentor character being held hostage, she needs to bring her evidence and the costume, blah, blah, blah. She goes to an underground cellar in suit, determined to bust some heads. There's a big bad in there I'm really tempted to make Blueblood (although I know that he wouldn't have the balls or the charisma to be the big bad) who figures out she's there and gets her to come down to negotiate. When he/she threatens Twilight, he/she doesn't know what she's getting into, because Dash figures out that she's in love with her and that she'd easily die if she could make sure that Twilight would be safe. Nothing being more dangerous than a pony ready to lose everything, tensions rise to a climax, and there's a standoff.
Just then, the rest of the mane six come in to kick some flank. Of course they'd put things together, and, with a lack of response from Celestia, had Spike-mailed Luna, who gave them the location of the raid, and they'd investigated stuff and blahblahblah. They still get overpowered, though. Rainbow Dash declares her love for Twilight as her last words, Luna and Celestia blaze in to kick some ass, showing how that Celestia was kinda a bitch, but she had everyone's best interests at heart and wasn't a part of the conspiracy. They all reconcile, Protagonist and Love Interest kiss, and all is right with the world. Also, everyone loves AJ again because no one can hate AJ. And the mentor character loves friendship. Kind of. Because he still must be dark and edgy.
...Well, that could have been a worse 1500 words, even though no one will pick this up.