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The Return of Queen Chrysalis
- In issue #3, the changelings land in a town and Chrysalis can be seen protectively holding one of her subjects in her lap, away from the inhabitants.
- During the climax of issue 4, the mane 6 and the Crusaders all talk about how their bonds of friendship and love give them the strength and conviction to do anything.
- During the fight, Sweetie Belle and Scootaloo sing Twilight's praises as she faces Chrysalis alone. Sweetie Belle thinks Twilight is the best unicorn there is, and Scoots wants to be just like her. Considering how much the two idolize Rarity and Rainbow Dash respectively, that's saying a lot.
- At one point in issue #4, Scootaloo comments on the lack of having a big sister. Later, we see Rainbow helping to rescue Scoots in the same vein as Applejack does with Apple Bloom, and Rarity with Sweetie Belle. The precursor of Scootalove from "Sleepless in Ponyville" is evident.
- In the same vein, when Twilight blasts Chrysalis across the room, Applejack and Rarity are holding on to Apple Bloom and Sweetie Belle to protect them. Guess who Rainbow is holding?
- After Twilight finally defeats Chrysalis, the CMC are rescued, and everypony meets Celestia and Spike outside, it's really heartwarming to see them all reunited around the campfire, finally safe after all they had to go through, especially when you consider that just a moment earlier Twilight was a hair's breadth from unwillingly turning into a monster that would destroy her own friends. A happy ending well deserved, indeed.
- Finally rescued from the kidnapping, Apple Bloom and Sweetie Belle can be seen sleeping snuggled against their big sisters by the campfire. At first, it looks like Scootaloo has just been completely shafted from the panel, as she isn't with Rainbow Dash or seemingly anyone else. But then...
The Nightmare Arc
- In Issue #6, Twilight catching the Fire Ruby Spike dropped as they were falling to the moon, even though a moment before she was telling him to forget about it.
Spike: Aw, Twilight, you're the best!
Luna: I'm your friend?
- When the Nightmare Forces try to convince Luna to sacrifice herself to save the others, the Mane Five quickly butt in and tell the Nightmare Forces that they're not going to take any more of their friends.
- Issue #7: Even though it was cruelly subverted seconds later, it's still pretty heartwarming to see Spike coming close to telling Rarity he loves her. She's more than just a crush to him now.
- Issue #8:
- Twilight's reaction to discovering Spike survived what happened in the previous issue.
- Right before the Nightmares' attack on Ponyville:◊
- The CMC are walking under Celestia's wings, offering their help. It gets accepted.
- Then, once the Nightmare Forces arrive, the Princess shields Scootaloo and Apple Bloom, while Sweetie Belle finds shelter under Cheerilee's foreleg.
- Luna tries to fight the Nightmare Queen alone, but is overpowered and falls. Celestia then rushes to shield her sister◊ with her own body.
- Everypony convincing Luna that her fight against the Nightmare Forces isn't her burden alone. Among these ponies is Trixie, who knows full well the regret Luna is feeling. Considering the number of fanfics where their roles are reversed, it's surprising to see it the other way around in an official work.
- The only ones able to momentarily reach Rarity are Spike, known for having a crush on her — and Sweetie Belle.
- Spike delivering the final lines prior to Rarity's liberation from Nightmare Rarity's grip. He gets extra points since the destroyed Fire Ruby repairs itself while Spike tells Rarity that she's everything for him and asks her to please come back home. After that, there's the final scene.
- Twilight's best memory of Rarity is also a heartwarmer. The unicorn is lying in bed, seemingly sick. Rarity arranges a cloth around her horn while levitating a tea pot with her magic. Twilight is looking up at her in an adorably grateful/affectionate way. From the glow on Twilight's face while she remembers it, it even counts as heartwarming to her.
Zen and the Art of Gazebo Repair
- Though #9 and #10 are mostly slapstick and making a Butt Monkey out of Big Mac, the end has Zecora convince a grumpy Big Mac that the fair had some high points in addition to being a massive obstacle. Big Mac thus decides to give up on the nails and enjoy himself.
- Cheerilie affectionately greets him, showing that they've apparently remained good friends since Hearts and Hooves Day.
- He also gets a kiss from a princess!
- Issue #11 gives us little filly Vinyl Scratch getting her cutie mark while standing on her brother's back watching Shining and his friends perform. She has the most adorable smile on her face.
- Issue #12 when Shining Armor finally stands up to Buck's arrogance and finds out, after all the time when Buck has been making him feeling so alone, that the rest of the school hates the Jerk Jock too and admires Shining far more.
- While Shining's nervous greeting to Cadance as he's leaving for his flugelhorn recital is played for laughs, issue #12 makes it heartwarming, by revealing that Cadance found his nervousness to be absolutely adorable.
- Shining Armor & Cadance's first kiss at the end of their flashback.
- The end of Cadance's story in "Neigh Anything." Cadance ends her account saying that she and Shining lived Happily Ever After. Shining corrects her, saying that they are still living happily ever after.
- The end of the story. Buck, who bullied Shining in school, arrives in the tea parlor, now in a relationship with Cadance's friend Lemony Gems and acting like a perfect gentlecolt with her. Then he and Shining turn around and make a friendly gesture at each other, which implies they've patched it up sometime over the years.
Ponies in Book Land
- The resolution of the bookworm problem: It turns out he's just upset that bookworms are never the heroes in any of the stories he comes across, and Twilight convinces him to become one himself by putting everything back to normal.
- When Celestia and Luna get some private time, Celestia admits the reason she kept her time in parallel universes a secret is that she's ashamed of her youthful indiscretions. Luna responds by nuzzling her and telling her she doesn't have to be perfect just because she's a princess.
- In the mirror world, Sombra gets one when he firmly says "No harm may come to her. I love her." regarding Celestia after it's discovered that fighting Evil!Celestia and Evil!Luna in any direct fashion will hurt the good versions. He's the one apparently in the most danger from whatever they've got planned, but his only concern is making sure that Celestia is safe.
- Celestia's flashback in issue 19 to when she and the Mirror World's version of King Sombra are rubbing noses, followed by their exchange in the following panel:
Celestia: I have to go.
Mirror!Sombra: I wish you didn't.
Celestia: I know.
- Sombra turning down a deal that could allow him and Celestia to be together, because he knows it would leave Celestia's world at the mercy of her evil counterpart.
- Twilight, still worrying about her possible destinies after learning more about Star Swirl and Princess Celestia, consults the mirror world's King Sombra for advice. The good king cheers her up by reassuring her that she doesn't have to force herself to be any particular kind of pony; all that matters is that she's a good pony at heart. That, and the mental image that Twilight gets of Star Swirl as an alicorn probably helped.
- Seeing Main!Celestia happy in the mirror world, if only for a little while.
- Main!Celestia reassuring Main!Luna that she didn't replace her with Mirror!Luna.
- Main!Luna forgiving her with a little hip bump and another joke about perfection. Adorable.
- A flashback in Issue 20 shows that despite chewing her out and sealing off the mirror portal, Star Swirl ended up forgiving Celestia, and admitted that he sympathized with her on the matter, but had to make a hard decision for the greater good.
- Mirror!Sombra catching Mirror!Luna after Mirror!Celestia attacks her. Likewise, Main!Celestia's concern for her sister after the attack's effects hit her.
- Celestia being perfectly willing to become sealed in crystal in order to stop Mirror!Celestia. In what she thinks will be her last conversation with her student, she tells Twilight how proud she is of her.
- Mirror!Sombra making a Heroic Sacrifice to save Main!Celestia and both Equestrias, using the Elements to absorb the evil magic of Mirror!Celestia and Luna into himself to restore the balance between the worlds. He knows that he'll be warped into a malevolent version of himself, akin to the main universe's version of King Sombra, but he goes through with it anyway. All so his beloved won't have to sacrifice herself.
Twilight Sparkle: (shedding tears) He... sacrificed himself.
- The last panels show Celestia and Sombra bidding farewell to one another in a Bittersweet Ending... and yet, as corrupted and dark as he's now become, the sight of Sombra shedding a tear shows that some part of him still loves Celestia, and thus may not be as irredeemable as his main universe counterpart.
- Trixie referring to the gang as friends, and assuring Chief Stablemaker that he can trust them.
- Trixie trying to become a better mare and help the police catch Rough Diamond. It turns into a tearjerker when Rough Diamond turns it into a Frame-Up though
- Applejack and the others being willing to give Trixie the benefit of the doubt.
- Babs relating to Trixie about how they're both former bullies. Trixie is so touched that her eyes glisten up and she sweeps the filly into a bear hug!
Just for Sidekicks 2: Pets to the Rescue
- The other pets cheering Angel up.
Annual 2014: Power Ponies Edition
- The Power Ponies managing to move past their fighting and become friends.
Annual 2015:Equestria Girls Holiday Special
- The Mane 5 doing their best to cheer Sunset up for the holidays.
The Twin Cherry Smackdown
- Cheerilee and Cherry Blossom resolving their differences and making amends.
- Cheerilee meeting her sister's fans, causing her to realize they're more alike than she thought in wanting to inspire kids.
Siege of the Crystal Empire
- Radiant Hope helping Sombra return and finally being reunited with him after over a millennium, even as she's Jumping Off the Slippery Slope in the process.
- When Chrysalis says Radiant Hope is dumber than she looks if she really thinks the Umbrum are peaceful, that's when Sombra finally loses his temper with her and snaps at her to shut up, or he'll petrify her. It's the first time Sombra has lost his temper, when Hope is insulted. Even if it isn't apparent off the bat, he still loves her.
- Hope's Even Evil Has Standards in trying to stop Sombra from both attacking the Princesses and killing the Mane 6. Despite her questionable recent actions, it's clear that deep down she's still the same mare who we originally saw in "Fiendship Is Magic".
- The ending of issue #36 (part 3 of Siege of the Crystal Empire) can count as this. King Sombra is having doubts about his plans to release the Umbrum when Twilight hits him with a magic blast. Despite protests from Cadence she shoots another at him, one that Radiant Hope throws herself in front of. You can see the hurt and terror on Sombra's face as he kneels in front of Hope. Possibly believing her to be dead he releases the Umbrum from their prison. It's possible he was holding off doing it for her sake, and with her gone he didn't see any reason NOT to release them.
- While many fans have their criticisms about the arc, many agree that Hope and Sombra's conversation about fate was nicely done. Whereas Sombra felt that he was destined to become a monster, Hope reminds him that she was destined to become princess, but threw that all away for him, proving that he always had the chance to Screw Destiny and still does. It all ends with him finally taking her words to heart by using the Crystal Heart to banish the Umbrum once again, rejecting his fate as a monster once and for all.
Sombra: (shocked) You four? Why are you helping me?
- Not to mention the ending. All four Princesses help boost Hope's magic enough to heal Sombra to the point where he's finally purged of his Umbrum essence and allowed to live life as a normal Unicorn. Furthermore, he and Hope ultimately decide to leave the Empire and go Walking the Earth in order to find and restore Amore as part of their atonement for all their past actions. Regardless of whatever flaws they may have had in this arc, the door is always open for them to make up for those in the future.
Cadance: I'm the Princess of the Crystal Empire. The Empire you just saved.
Twilight Sparkle: And it was your friendship that saved the day. Friendship is kinda my thing.
Celestia: If Twilight is a believer, then so are we, right, sister?
Luna: I would follow Twilight anywhere.
- Diamond Tiara and Apple Bloom talking as they play on the swings. Then, when Apple Bloom's swing breaks, Diamond immediately asks if she's okay.
- Before Twilight and Luna enter Accord's mind, Celestia tells them both to be careful, and gives her little sister a kiss on the cheek.
- When Twilight and Luna discover the last remnant of Discord in Accord's mind, Twilight actually hugs him. Discord returns the favor, and tells both Princesses that it's good to see them.
- Discord chose to become Accord because he believed he could fit in better with the ponies that way. This shows how far Discord has come, in that he was willing to give up his very self in order to gain acceptance.
- The heartfelt speech Starlight Glimmer uses to convince Accord of his wrongdoings, pointing out that true friendship isn't about everyone being the same, but forming a connection despite their differences. Every word is a testament to how far she's come:
- Starlight Glimmer: Harmony is many different notes, all coming together... to make something greater. We need those different notes... that wild and unpredictable music... to make something beautiful.
- After Discord is restored to his true self, Fluttershy welcomes him back with a big hug.
- Applejack apologizing to Discord for how he was treated at the beginning of the arc.
- Applejack: I just wanted to sayŚwell, sorry for makin' you feel unwelcome, Discord. You may be a plumb crazy critter, but dang if that ain't what we love about you!
- The final page of the story features a splash of several of the series' characters gathered together, with the immortal line "friendship is magic!" Fitting, considering it was the fiftieth issue.
- In the bonus story "For The Pony Who Has Everything", Discord puts a lot of time and effort into getting Celestia a truly unique gift.
- After Discord disguises her a Pegasus, Celestia heads straight for Ponyville, wishing to interact with her beloved subjects like a normal pony.
- At the end of the story, Celestia thanks Discord for his gift, calling him a "good friend".