The sequel to Parting Words.The story begins at the start of the season 3 finale and contains a second divergence from canon. Instead of only Twilight ascending, all of the Mane six become Alicorns. Now Celestia and Luna have a new job for the Mane 6: To move the Great Plan forward, they must go out and track down all the other alicorns that they believe are manifesting all over Equestria.By the way, Luna thinks it might be a good idea if they focused first on finding an alicorn stallion or two...Can be found here.
The Ahnold: Pinkie Pie's guards, former bouncers, intentionally act like this. The sight of them sends Luna to a series of cold showers.
Amazon Brigade: Rarity's Radiant Guard are almost entire made up of mares. They double as Ladies of War, though she apparently took them mostly so she could use them all as models for her dresses.
Also note that Celestia's Day Guard includes mares as well (many of whom were transferred to the Radiant Guard), but they were largely disguised as maids. Still just as deadly as the stallions.
Badass Adorable: Fluttershy's kid brother Breezy Shy, a.k.a. Bishi. As shy as her... and a trained martial artist (only uses it in self-defense, of course.)
Poor Luna has a HILARIOUS one on ALL of her bodyguards.
Inverted with Fluttershy, with all the guards having a crush on her.
The Bet: Before meeting Fluttershy's folks, her friends take bets on which one will be 'the loud one'. (Dash, knowing the answer, abstains.) Babs wins the pot by correctly guessing that the whole family acts just like Fluttershy.
Born Lucky / Born Unlucky: It turns out that Pinkie Pie's unusual abilities are due to an innate ability to perceive and manipulate probability. It's a extremely rare variation of Earth Pony magic, unfortunately they're most commonly known as "Ill-Starred" and thought to be jinxed.
And Celestia and Luna have learned it, and Luna gets the unfortunate job of mentoring Pinkie.
Broken Pedestal: In chapter 13, the Wonderbolts lose significant respect for Rainbow Dash when they think she bought her way onto the throne. After Spitfire chews her out in chapter 15, RD's pedestal quickly crumbles. Thankfully, both are rebuilt in the next chapter after a nice, long talk.
The Bully: Pennyworth and his two surprisingly thuggish companions, Bullhorn and Air Drop, along with Marzipan, Ruby Drop, and Ivy.
This also serves as a bit of a callback to the prequel, where the Celestia wondered where the attitude of "Fighting back makes you just as bad as the bullies" comes from. Here, we see one source of where this attitude comes from.
Crazy-Prepared: Breezy Shy brings his martial-arts training shoes to the Junior Gala just in case he has to defend himself. When the bullies from Babs' school start to threaten the Crusaders, he changes into those shoes and handily beats the stuffing out of their leader.
Twilight and Flash Sentry have opposing definitions of the term. For Twilight, it means everything is punched into an itemized checklist, while for Flash, his preparation is in his lack of preparation.
Color-Coded for Your Convenience: Everything relating to the Mane Six princesses are color coded accoring to their coat color. From their elements up to their airships.
For Want of a Nail: A blink-and-you-miss-it example: Chapter 5 reveals that Spike still has Peewee.
For whatever reason, different circumstances mean that Equestria Girls didn't happen in this universe. Though, Celestia's comments when introducing Twilight to Flash Sentry reveal that Sunset Shimmer did still break into the Crystal Palace (and was promptly arrested).
There's also the prequel's version of how Sombra was handled, where he took maybe a few minutes (tops) to defeat utterly. In a similar vein, Twilight analyzed the riddle that Discord gave her, and found the elements almost immediately, leaving Discord standing alone in the maze for over an hour before he tried to find the Mane Six... who were now decked out with the Elements and were waiting for him.
Living Forever Is Awesome: Celestia and Luna are tired of outliving everypony else, but otherwise they hold this opinion. Thus, they ask the Mane Six to assist them in their quest to make everypony immortal.
Living Lie Detector: Applejack's Elemental powers give her a version of this that overlaps with Blessed with Suck. She can tell when she isn't getting the full story, even if whoever's talking to her is telling her everything they know, and her Element won't let her rest until she gets all the facts.
Marry Them All: Ponies can form herds (or at least used to, fairly recently. It's far less common in the present.) Sweetie Belle thinks this'd be the perfect solution to all the CMC crushing on Breezy Shy.
Mayfly-December Romance: Luna had one about 500 years before her banishment, she swore not to try again but after 1,500 years of not getting any she's feeling a bit tense. And as of chapter 7 Cadence and Shining Armor's marriage is no longer one.
"One hundred bowling balls... three hundred and sixty five 'happy pine tree' carriage air fresheners... twenty four ACME brand cannons... a blender... six hundred boxes of instant cake mix... one ton of confetti... one hundred forty four pink flamingos... a bag of marbles... five bags of fortune cookies... a lug wrench... a box of elephant prophylactics... Five cans of purple paint... five cans of yellow paint... five cans of PINK paint... one jelly-bean pooping plastic moose... five spare tires... a rubber life raft... eight thousand Kewpie pony dolls... a giant flyswatter...a toaster... one pair of each kind of 'Groucho Marks' glasses... one live parrot... one dead parrot, stuffed..."
Oh Crap: When Pinkie Pie becomes an alicorn, she realizes she can do magic. This trope is Rarity's reaction.
Mass "Oh, Crap!": The bullies get this when they realize the CMC were telling the Truth about being related to the new Princesses... via a Angry Applejack showing up after hearing them start to plan getting revenge.
Of Corset Hurts: First thing Dash does after the ceremony's over is strip off her girdle and advise Scootaloo to never let anyone talk her into wearing one.
Pinkie Pie's family have basically ignored her for years, due to her differences.
While Rarity and Sweetie Belle's parents are generally nice, they have a tendency to go off on long trips and leave Sweetie Belle in the care of various sitters.
The Plan: Celestia and Luna's plan is thus: find other alicorns, and with a combination of their magic, insight, and (ahem) bloodlines, abolish old age.
Poor Communication Kills: Well, not kills, but it does lead to a lot of friction between the Wonderbolts and Rainbow Dash. Spitfire claims that Celestia told her about their new assignment... which Rainbow Dash assumes is that they've all been briefed on "The Plan" (see above). Celestia actually told Spitfire that their mission was to keep an eye on Rainbow Dash, and that Dash would provide further details later. As such, the Wonderbolts feel like they're babysitting a spoiled fangirl, while Dash can't understand why they don't like her.
Ragtag Bunch of Misfits / Reassigned to Antarctica: The majority of Applejack's guard, The Roughnecks. Aside from the usual discipline problems there's also a few donkeys, a crystal pony, three batponies, a gryphon, a zebra, even a diamond dog.
Rank Up: When Twilight inducts the first bunch of Royal Guards into her branch (the Twilight Guard), Celestia's last act as their commander is to promote Flash Sentry on the spot from Lieutenant to Captain, pointing out that he is Captain of the Guard anyway, so he should have the rank to prove it.
Reaching Between the Lines: In Chapter 14 Pinkie Pie reaches through the magic mirrors they're using to communicate, and gives Rainbow Dash a hug. Naturally everypony else wonders how she did that.
"The Reason You Suck" Speech: Chapters 15 and 16 have a back and forth of this: The latter half of chapter 15 involves Spitfire chewing out Rainbow Dash because she thinks Dash didn't 'earn' her position as a Firebolt or princess. Chapter 16 swings the other direction with Dash reminding Spitfire that all the deeds she had done, including her work with the Elements of Harmony, her Sonic Rainbooms, as well as saving Spitfire's life, were all based on her own merit. While every time the Wonderbolts have been called to do anything more than put on a stunt show they'd failed spectacularly.
Screw the Rules, I Have Connections!: Babs' bullies always got off scott free due to having wealthy and influential families. Unfortunately for them, Babs is now technically royalty. They didn't realize that until after they tried to attack her AND the CMC and Bishi, three of which are royalty, being immediate family of three princesses, and one practically being an apprentice to one. So, not only did they get their flanks kicked, they also got on the bad side of the Princesses, shipped off to Sweet Apple Acres to do hard labour or not get fed, and cut off by their parents due to royal decree.
Screw the Rules, I Have Money!: Pennyworth and Babs' other bullies are used to getting away with their actions due to this. As part of their punishment, they get cut off.
Both Screw The Rules tropes are also hinted at heavily by the Wonderbolts, wondering who that mare is in charge. This doesn't go over well.
Shared Family Quirks: Not only do they all look alike, they all act in the same shy, introverted fashion as Fluttershy. Also, surprisingly, they're all geniuses with their special talents with Fluttershy's mother and father both seemingly inventing hydroponics in Cloudsdale. Yes. Fluttershy's mother grows plants on clouds.
Ship Tease: The captain of the Guard appointed for Twilight by Celestia is Flash Sentry — and Twilight seems to be developing a crush on him.
Sibling Team: Three out of the six princesses are this. With the exclusion of Twilight and Pinkie Pie, we have:
Sweet and Sour Grapes: Due to her ascension to alicornhood, Rainbow Dash cannot become a Wonderbolt. She can, however, command them... and since the titular hunt will be done undercover, she can fly with them as part of her cover story.
Take That: The whole idea of a "wingboner" gets called out as a ridiculous myth spread by unicorns and Earth ponies. The idea of a unicorn's horn being "Sensitive" is called equally silly.
Chapter 6 has several towards a few of the more iconic moments in the series, such as the Winter Wrap Up (letting the snow melt would probably be more beneficial), The Running of the Leaves (two ponies squabbling shouldn't be enough to prevent leaves from falling; wind would be more efficient and easier), Weather Factories (making individual snowflakes by hoof is remarkably inefficient), and draining the reservoir via tornado (evaporation would work just as well, with much less time, energy, and effort for all involved).
Too Dumb to Live: You would think Pennyworth and his goons would realize that the CMC were telling the truth, seeing that them being nobility (or having as much money as them) would be the only way they would've gotten into the Junior Gala in the first place.
Trickster Mentor: In spite of halting her 'cryptic mentor' tendencies with Twilight Sparkle, Celestia still tends to be enigmatic and manipulative with a few things, not the least of which includes selecting a host of male guards for Twilight and Fluttershy in hopes that they find their 'super special somepony.' Kinda backfires with the Wonderbolts when she fails to fully debrief them on their 'true' mission with Rainbow Dash.
What the Hell, Hero?: After having had enough of the Wonderbolts giving her the cold shoulder and badmouthing her behind her back, Rainbow Dash confronts Spitfire about it. When the latter says that Dash is a show off who hasn't earned anything she has, Dash snaps and gives her a scathing "The Reason You Suck" Speech, pointing out how hard she worked to earn everything she has, not to mention has saved the world several times, whereas the Wonderbolts are either no-shows or ineffective in a crisis, and Spitfire herself is as guilty of being self-absorbed as she accused Rainbow Dash of being. Spitfire admits Rainbow Dash is right, and they make amends, with Spitfire helping Dash mend fences with the other Wonderbolts.
Who Wants to Live Forever?: Or rather, who wants to live alone forever? Celestia and Luna have no problems being immortal, but having to watch, again and again, the ponies close to them grow old, feeble and die after such a short time together is truly heartbreaking for them. This is what kicks off the main plot of the story — to find more Alicorns and eventually find a way to pass the gift of immortality on to everypony.