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Happens with Pinkie Pie and Rainbow Dash so many times it's easy to lose count, jokes about the latter's rainbow-coloured mane aside.
"Griffon the Brush Off" plays exactly like Pinkie Pie trying to vie for Rainbow Dash's attention after her old flame shows up. This includes Gilda (see below) violently preventing Pinkie from intruding on her time with Rainbow, and Twilight outright stating she thinks Pinkie is jealous of Rainbow and Gilda's relationship. And at the end, after Gilda reveals herself to be a total bitch, Rainbow reaffirms that she'd much rather be with Pinkie. It even starts with something very closely resembling Pepe le Pew chasing Penelope Pussycat, complete with Pinkie doing his little love hop. Netflix's description of the episode says that Pinkie becomes a "third wheel" between Gilda and Rainbow.
Pinkie's Rainbow Dash obsession is revisited in later episodes; it's almost a running gag that she's Rainbow Dash's Stalker Without A Crush (with similar themes to a stalker with a crush), with Pinkie affectionately calling her "Dashie" (something almost nopony else does), following her damn near everywhere (particularly in "Over a Barrel" and "Party of One"), and having a severe case of No Sense of Personal Space even by Pinkie standards.
In "Party of One" the pony sent to fetch Pinkie for her surprise party is Rainbow Dash, entering with a brief shot showing Rainbow Dash's face framed in the heart on Pinkie's door. Rainbow Dash tries to force Pinkie Pie to move by shoving her forehead in Pinkie Pie's butt, Pinkie then sits on Dash's face, and Rainbow Dash says they'll have to do it "the hard way".
Right at the end of "The Super Speedy Cider Squeezy 6000", Pinkie offers one of her mugs of cider to a really crushed Rainbow Dash after the poor Pegasus finds the cider running out yet again. Throughout most of the episode, Pinkie acts extremely oblivious to Dash's annoyance at not being able to get any cider, and while gushing about the cider she just drank, Pinkie leans further and further onto Rainbow Dash, until she's literally draped over Dash's back.
In "Too Many Pinkie Pies" Pinkie initially is unable to choose between Applejack and Rainbow Dash for the afternoon, but once she has her first clone immediately chooses to be with Dashie herself and sends her clone to Applejack. Rainbow Dash is willing to be far more patient with Pinkie's antics than she normally would be for other characters, even as she states she just wants to relax while Pinkie is being her usual self. In response to this, Pinkie actually goes quiet, something she almost never does unless things are serious.
In "Daring Don't", Pinkie hugs Dash and rubs up against her for far longer than is strictly necessary, before Dash pushes her away.
Pinkie Pie is infuriated when she thinks Rainbow Dash has been hurt in "Rainbow Falls", and threatens payback on who/whatever hurt Dash. In the episode, she also acts as the Ponyville Team's single cheerleader, and loudly cheers on Dash as she flies the relay race.
In "Pinkie Pride", Pinkie and Dash hold hooves right before Pinkie pins Dash to the ground and ends up in quite aninteresting position. Pinkie spends the whole episode desperately trying to impress Rainbow Dash and make her happy, only stopping when she realized that her efforts were only making Rainbow Dash less happy. She also treats Rainbow Dash's "birthaversary" as a veryserious matter, moreso than most of her parties.
Rainbow Dash and Fluttershy, Childhood Friends for longer than any of the other mane six members have even known each other, are frequently shown to be very close.
"The Super Speedy Cider Squeezy 6000" opens with Rainbow Dash barging into Fluttershy's room and pulling the blanket off of her as she lies in bed, causing the latter to blush and cover her chest (albeit rather pointlessly). Rainbow Dash also deciding to cut Fluttershy in on her deal to hoard cider (over all her other friends) says a bit, as does Rainbow letting Fluttershy go ahead of her in line.
"Sonic Rainboom" opens with Fluttershy recapping "the elements of a good cheer" that Rainbow Dash has been teaching her: "loss of control", "screaming and hollering", and "passion". It's given out of context with no explanation until afterwards, so it kinda sounds like she and Rainbow Dash are talking about... something else.
Rainbow at one point tells a distraught Fluttershy "But I need you!" while dramatic, emotional music plays. Then, after Fluttershy runs off, Rainbow Dash reaches out with her hoof, her disappointment and frustration mimicking a lover being disappointed in their other half. Fluttershy's breakdowns themselves seemed to be a combination of self-doubt and being upset for disappointing Rainbow.
Throughout the episode, Rainbow was oftentimes making intimate physical contact with Fluttershy. Hugging her, bringing a foreleg around her shoulders, touching her cheek, holding her at arm's length, and even sharing the equivalent of a high five.
Fluttershy showing up at the site of the reservoir during Tornado Day, just to give Rainbow moral support. Despite that she felt terrible and didn't even want to participate in the slightest, she still showed up to support her.
Rainbow almost immediately turns the praise to Fluttershy when Spitfire was congratulating her, even going as far as referring to Fluttershy as her "number one flyer". It's a Crowning Moment of Heartwarming for so many reasons and really shows how much Rainbow cares about Fluttershy.
"Dragon Quest" opens (what is it with these two and episode openings?) with Rainbow Dash and Twilight Sparkle trying to get Fluttershy to go see the dragon migration, when Rainbow Dash mentions when she and Fluttershy went to go see the butterfly migration together. Casual outing between friends, or really boring date? On top of that, Dashie has a picture of them on the migration trip together that she has been carrying around. Photo to remember the date, perhaps? (While probably unintentional, Rainbow's line of vision in that photo is actually directed right at Fluttershy's cutie mark. So she actually was watching butterflies, just not the ones passing in the air.)
During the attack of the changelings in "A Canterlot Wedding - Part 2", Rainbow Dash almost kisses Fluttershy on the nose when helping her up. What sells this is that Fluttershy briefly closes her eyes as though she expected to be kissed.
Their first meeting (as shown in "The Cutie Mark Chronicles") is straight out of a Rescue Romance, with Rainbow rushing in to protect Fluttershy from the bullies tormenting her, and Rainbow herself saying that she was "defending Fluttershy's honour".
"Keep Calm and Flutter On" not only has Rainbow acting more like a jealous and overprotective girlfriend when she sees Fluttershy being nice to Discord, but Fluttershy also called her "Dashie", something she never did before.
"Daring Don't" has yet another opening with the two. An excited Rainbow Dash constantly touches Fluttershy in some manner, right to holding her hooves.
There was a bit going on between them in "Rainbow Falls", such as Fluttershy (along with Bulk Biceps) being part of Rainbow's three-pony pegasi relay team, and saying she was competing for Rainbow (and Ponyville, as well).
In "Trade Ya" Fluttershy does everything in her power to make Dash happy by getting her the Daring Do book she wanted, and when Dash realizes she's traded Fluttershy for the book she immediately fights to get her back and doesn't give the book a second thought. Plus she gets Fluttershy the bird call she wanted at the end.
"Fall Weather Friends" might as well have been called "Belligerent Sexual Tension: The Episode", with the two going to ever greater lengths to best the other and prove their superiority. Even the lesson at the end wasn't that they were constantly competing, but them taking it too seriously was threatening their relationship, and the episode ends with them galloping off into the sunset together.
In "Bridle Gossip", Applejack fashions a crude set of bit-and-reins and rides an upside-down flying Dashie around.
In "The Mysterious Mare Do Well" Rainbow Dash "immortalizes" Applejack as her best friend, in the process bringing their faces very close together (which is conveniently obscured by a camera flash). So close, in fact, that it can easily mistaken for them kissing.
In "The Last Roundup", Rainbow Dash is depicted as the one pony closest to Applejack, including being the first one to notice when she's lying, and tackling her at the end of the chase scene, with a briefly triumphant expression.
Their human counterparts, when compared to the other girls post-break-up, the way Applejack talks about Rainbow Dash makes her sound like a bitter ex-girlfriend. The two are also the only ones to apologize to each other on-screen and they even seal it with a hug.
When A.J is forced to sacrifice her prize apple in "Bats", Rainbow is the only member of the group who actually takes a moment to console her over it (as opposed to say, Twilight, who was the one responsible for Fluttershy's transformation in the first place).
In "Return Of Harmony Part 2" a newly restored Dash tackles A.J to the ground and pins her down (to ask what the situation is, but still).
Our heroine, in her unending quest for friendship, can get very close to the ponies around her.
As pictured above, in "Lesson Zero", Twilight Sparkle asks Rainbow Dash not to "hide her feelings" by cupping her face with both forehooves in a manner that could be interpreted romantically when taken in combination with her words. Humorously, the context is that Twilight is actually talking about Rainbow Dash's feelings towards Applejack.
Near the end of the episode Pinkie Pie nuzzles Twilight, the only pony to do so. (Twilight also nuzzled Applejack and Rainbow Dash respectively in "Dragonshy" and "Over a Barrel".)
Rainbow Dash:(to the pets) Alright, now these games will determine which one of you has the most important qualities I'm looking for in a pet. Speed, agility, guts, style. Coolness. Awesomeness. And radicalness. Twilight Sparkle: Aren't those all the same thing? Rainbow Dash: You would think that, Twilight. And that's why you would never qualify to be my pet.
"The Ticket Master" has Rainbow hovering by Twilight when asking about the ticket along with this line:
Twilight: Rainbow Dash! Were you following me? Rainbow Dash: Yes-I mean no-I mean, maybe!
In "A Canterlot Wedding Part 2", Twilight asks Shining Armor how he managed to get Cadance to marry him. He says that he mentioned that if she did, she'd get an "awesome sister". So Cadance married a guy just to get closer to his sister?
In Part 1, Twilight's first reaction to reuniting with the fake Cadance is to wiggle her rump in her face. Later, the real Cadance returns the favour, although the actual wiggling occurs off-screen. (Sure, It Makes Sense in Context, but wow.)
In "Three's a Crowd" Twilight makes quite a big deal over how happy she is that she and Cadance will get to spend time together, and how frustrated she is that Discord tries to get between them.
During the "You'll Play a Part" song from "Twilight's Kingdom - Part 1", Cadance tells Twilight "You're gifted and you are strong," at which Twilight blushes.
Twilight is intensely reverent of Princess Celestia, well beyond even the usual level of grovelling obedience most ponies display towards her, and is utterly terrified of disappointing her or seeming "unworthy" in any way (as shown in "Swarm of the Century", "Bird in the Hoof", and especially"Lesson Zero").
In her flashback in "The Cutie Mark Chronicles", Twilight says that Celestia raising the sun was "the most amazing, most wonderful thing [she's] ever seen," and was the inspiration for her to pursue both magic and research as passions.
Twilight says she wants to go to the Grand Galloping Gala to talk magic with Celestia, but she has already been regularly doing this by sending friendship lessons by Spikemail◊. Their wording for each other can be interpreted as more than professional:
Princess Celestia: Well, I want you right by my side the entire evening, so we'll have plenty of time together. Twilight Sparkle: That's just what I was hoping you'd say.
"The Crystal Empire - Part 2" shows that Twilight's worst, deepest fear is Celestia rejecting her and no longer being able to be her student.
When Twilight sees Celestia in the alternate dimension she gets transported to after finishing the spell in "Magical Mystery Cure", her first reaction is to run over and give her a hug. Even when Twilight is transformed into an alicorn princess, she is upset at first, because she thinks she won't be Celestia's student anymore.
Princess Celestia: You may no longer be my student, Princess Twilight, but I hope you know that I will always be here if you need me. Just as I hope that you will always be there when I need you.
After Cadence, Luna, and Celestia transfer their magic to Twilight for safekeeping in "Twilight's Kingdom Part 2", Twilight's first instinct upon recovery is to rush over and hug the exhausted Celestia comfortingly. She's even crying as she does so.
At the end of "Feeling Pinkie Keen" the two of them are holding their hoofs together while they're reconciling.
Pinkie and Twilight get a bit at the end of "Trade Ya" when Pinkie reminds Twilight of the sentimental value of the books she's trying to get rid of.
Twilight: ...And this is the book I got on the day I met you.
In "Luna Eclipsed", Twilight lures Pinkie into a dark alley with candy, and when she's out of view of the crowd she jams her against a wall with a hoof to her mouth and tells her "No shrieking. No screaming or squealing either." Twilight then shows Pinkie she isn't alone, at which point Pinkie flees in terror, prompting Twilight to tackle her and pin her to the ground. note Context? What's that?
At the very end of "The Crystal Empire - Part 2", Rarity winds up holding Twilight's hoof.
Trixie and Twilight have amazing Foe Yay in "Magic Duel", and by the end of the episode they manage to become friends.
Twilight Sparkle: I can't stop thinking about Trixie!
During "Dragonshy" Applejack saves Twilight's life from an avalanche and gets a neat little nuzzle in return for her heroics.
The Equestria Girls version of Twilight is surprisingly flirty in the "Perfect Day for Fun" short. First she drags Fluttershy around the carnival by the hand as though they're on a date. Then, when the group has got together and they're all taking pictures in the photo booth, one picture depicts what can only be described as Twilight copping a feel! She has her hand very clearly touching Applejack's chest (who in response looks very shocked). Finally at the end, the group ride a ferris wheel together and Twilight has her arm around Fluttershy's shoulder, again in a very "date-like" way.
In My Little Pony Equestria Girls: Rainbow Rocks Twilight and Sunset Shimmer have a moment of personal bonding in the kitchen, including the two of them speaking at the same time and smiling at it, they sing a duet together, and at the end of the film Sunset writes to Twilight "I miss you already. Hope you can visit soon." The kitchen scene also includes Twilight calling out to Sunset as she goes to leave, then backs down and says "nevermind". Can't Spit It Out?
Rarity: Oh, I just so wish it [the crystalization] was permanent! Did you see how my mane just absolutely sparkled? Applejack: But, good things are better when they're a "rarity" (winks). Rarity: Awwwwwww (giggles).
The Rarity issue of the the micro series comics shows Rarity going on vacation... and bringing along a picture of Applejack to put on her nightstand.
In "Green Isn't Your Color" Rarity seems more upset and jealous about Fluttershy's career forcing her to miss a (for lack of a better word) date with Rarity than Fluttershy accidentally becoming part of the fashion spotlight instead of her.
"Filli Vanilli" shows Fluttershy and Rarity giving an adorable nuzzle. Both episodes feature Rarity putting a lot of effort into trying to gently coax Fluttershy out of her shell, compared to most of the other characters who are usually either far more blunt about Fluttershy's hang ups if not outright oblivious.
The start of "Sweet And Elite" features Rarity profusely kissing Princess Celestia's hooves, thanking her for everything. For her part Celestia looks highly uncomfortable with the affection... while nervously glancing between Rarity and her bed.
In the first episode, "Mare in the Moon", Rarity drags Twilight to her house to forcibly dress her in several dresses, and starts gushing over her after learning she's from Canterlot, and gets really close to her cheek to cheek saying they're going to be "the best of friends".
The final scene of "The Crystal Empire" involves Rarity starting off the 'Twilight is awesome' song, making goo goo eyes at her throughout, and eventually cuddling with her inside a heartshaped window.
Lyra Heartstrings with Sweetie Drops/Bon Bon
Sweetie Drops/Bon Bon and Lyra Heartstrings, two background mares who appear together in many episodes, are widely assumed to be either best friends or a couple. Second season episodes include apparently deliberate nods to this phenomenon:
Wide shots of the town common early in "Hearts and Hooves Day" feature a number of pony pairs standing around. Lyra and Bon Bon are among these pairs, though there's another Bon Bon paired with Shoeshine.
A blink-and-you'll-miss-it moment in "Fall Weather Friends", in which Derpy Hooves (before the animators started intentionally derping her eyes) drops a rose, which Fluttershy just happens to catch.
Fluttershy reaches near Even the Girls Want Her status in "Green Isn't Your Color". Rarity wants her to model for her in the first place because "nopony is going to have [Fluttershy's] elegance and poise". Twilight says that "on her own Fluttershy could never do something unattractive" (hence her plan to use magic and make her do something unattractive). Photo Finish spends almost her entire appearance fan-girling over Fluttershy ("Yes! Even her sneezes are graceful!"). And the main reason Fluttershy hates being a model is the hordes of mostly female fans that flock to her wherever she goes.
In "Hearts and Hooves Day", Twist gives her holiday card to a gray colt, and they hug. This visibly disappoints another filly (Tootsie Flute), who had been looking in their direction. Was that filly hoping to give her card to the colt, or to Twist? Meanwhile, yet another filly (Princess Erroria) gives her holiday card to Diamond Tiara, who seems surprised by this attention.
In "Hearth's Warming Eve", Princess Platinum seems very close to her assistant/advisor Clover the Clever. Platinum yells out "Clover the Clever! I NEEEEEEEED you!" in Clover's introduction. Later, she tells Clover she doesn't mind it when Clover "stoops down" for her (yes, she's talking about crossing a stream, but hiding implications behind stuff like this is prime Radar material), before riding Clover across said stream while Clover is wearing a bridle. After the leaders thaw out, the Pegasi and Earth ponies share hugs and high-fives; Platinum and Clover, however, nuzzle. Since the ponies are also portraying the characters in a play, this could be considered another Rarity/Twilight moment.
Gilda has the same raspy voice and passion for athleticism that leads so many fans to think Rainbow is a Lesbian Jock, coupled with an extreme level of jealousy that quickly turns violent when Pinkie tries to get anywhere near Rainbow. She thinks a series of relatively harmless pranks are deliberate attempts by Pinkie to drive her away so she can keep Rainbow for herself, but when Rainbow reveals she was the one who set up the pranks Gilda is furious, and demands that Rainbow choose between them now. When Rainbow doesn't choose her Gilda is visibly hurt, and leaves immediately after tossing out a half-hearted insult.
Scootaloo has major Hero Worship towards Rainbow Dash, frequently to an obsessive level ("I'll do whateveryou want!"), with "Sleepless in Ponyville" basically being "Scootaloo stresses out attempting to impress her crush." It's mostly justifiable by Scootaloo wanting Rainbow to be her big sister, but Apple Bloom and Sweetie Belle don't display anywhere near the level of awe and admiration for their sisters that Scootaloo does for Rainbow.
Since "The Mysterious Mare Do Well", she's literally fangirling over Rainbow Dash whenever she has a chance to be with her. When Dash was wavering a flag as a demonstration in "Flight to the Finish", Scootaloo watched with sparkles in her eyes. And once we see Scoots' house, guess which pony she has multiple posters of?
"The Mysterious Mare-Do-Well" begins with a meeting of the Rainbow Dash Fan Club, with the first order of business being coming up with a word to properly describe Rainbow Dash's awesomeness ("awesome" just isn't good enough.) Naturally, Scoots is the leader of said fan club.
In "Keep Calm and Flutter On" Celestia has so much faith in Fluttershy's abilities she's confident she'll be able to induce a Heel-Face Turn in the local Mad God. One part of the scene even looks very much like wedding vows if taken out of context.
"Read It and Weep" opens with Rarity and Pinkie Pie swooning as they essentially watch the "dazzling" Rainbow Dash work out. Twilight soon joins them.
In "Daring Don't" Rainbow Dash openly proposes herself as a housewife to A.K. Yearling, the author of the Daring Do books she is a fan of. After she learns A.K. is Daring Do, she tagsstalksalong and violates her personal space quite often◊.
Twilight Sparkle: A.K. Yearling just might be my favorite author. I know everything about her. Where she grew up, where she studied literature, where she wrote the first Daring Do book... Rainbow Dash: Where she lives? Twilight Sparkle: Uh... no, though I could probably find out somehow. Why? Rainbow Dash: Don't you get it? The new book is obviously delayed because she needs help dealing with whatever everyday nonsense is distracting her from spending her every living breathing second writing! So I– I mean, fans like me, can get to read the new book ASAP! Think about it! We could help her with her laundry, buy her groceries, cooking her meals, whatever! Now, who wouldn't appreciate that? Twilight Sparkle: Hmm, I don't know... What she probably wants most of all is respect for her privacy. Rainbow Dash: She can always just say no. Twilight Sparkle: Mmh... I suppose you're right... Rainbow Dash: Of course I am. So... how's about getting that address?
In "Twilight Time", when the crowd of fillies start snapping photos of the CMC with Twilight, Scootaloo starts posing, including pulling Sweetie Belle to her side like they're a celebrity couple.
Apparently, Scootaloo watches Apple Bloom sleep, and thinks she does everything "with sass".
At the start of the "Battle of the Bands" song from Equestria Girls: Rainbow Rocks, Adagio Dazzle walks past several students (both male and female) and, um... strokes them all in a rather sensual way. There's extra emphasis placed on her cupping Trixie's chin.
The Theme Tune Extended (included as a sing-along on the DVD The Friendship Express) has such wonderful character puns, sung from Twilight's perspective, such as "Once smitten, twice Fluttershy", "You are the Applejack of my eye", "A heart that shines so beautiful, a Rarity to come by", and perhaps best of all, "As easy as Pinkie Pie."
In Adventures in Ponyville, when the player's (female) pony talks to any of the Mane Six, they'll sometimes say "Pony up!" to her. Unlike everything else they say to her, the speech balloon used for "Pony up!" is lined with a couple of hearts, making it seem like the Mane Six are casually flirting with the player's pony.
The German magazine comicDer Stern der Winterträume, Scanlated as The Star of Winterdreams, endswith the Mane Six sleeping together by the fireplace. Rainbow Dash is on her side, turned towards Applejack.
Box-art◊ for some of the toys includes Rainbow Dash looking at Pinkie Pie while their faces are framed together in a heart symbol.