WMG / The Great Alicorn Hunt

Celestia is pregnant

As displayed in the comments of Chapter 38, there are several moments with Celestia, which, taken together, paint a picture:

"Goodness, my moods are all over the map today," Celestia said, wiping her eyes with a wingtip. "Take that as a warning, dear Twilight; immortality is no protection against the ravages of hormones." - Ch 12

[Said by Celestia, as the plunder vines grow wild in the Everfree Forest] "Oh blast it, I'm in no condition to deal with this—" - Ch 17

Sunset Shimmer gave her former teacher a critical eye; she could barely help thinking that the Alicorn princess had gotten a bit... thicker around the middle. - Ch 18

"Ooo, pickled peppers?" Celestia said. "Send me some?"Luna stuck out her tongue and wrinkled her nose. "Thee and thy cravings..." - Ch 30

Celestia was enjoying a brief hour or two of respite. She was lounging on her divan on the balcony while one of her guard— a thestral who had transferred to the day watch— massaged her hooves. "Oof," she murmured. "Right there, Duskfall... blast, my frogs have been aching these past few..." - Ch 38

For some reason Celestia's mirror only showed her from the neck up... - Ch 51

It's possible that the author is simply trying to lead readers the wrong way, but it seems like the sort of twist that Ralph Hayes, Jr. works into his stories.

• Additionally, this would help explain why Celestia has arranged for Luna to be surrounded by exactly the kind of stallion Luna finds most desirable. She's trying to get Luna to slip up and break her oath before Luna can find out that Celestia has managed to get herself with foal.
• Something else to consider: unless Celestia broke her word and "robbed the cradle", the only immortal males around the probable time of conception are Shinning Armor (who is involved with Cadence) and Discord. Unless there was some herd thing going on (like what Celestia mentioned to Sweetie) there was only one available male. Add that Discord hasn't been seen far from Celestia and....

The Mayor of Windy City is behind the Crownbreakers

As a False Flag Operation to take down the Nobody's Fools. Think about it — he's stated to be obsessed with taking them down, and as of Chapter 46 has jumped on the chance to have them arrested when the slightest evidence suggesting they're connected to the Crownbreakers surfaces. But, Scootaloo knows the group well enough to know that they would never be involved with that sort of thing. Plus, it's stated that no one knows who the actual leader of the Crownbreakers is.

So, it seems likely that the Mayor set this whole thing up just to get rid of them. And it's going to bite him in the ass.

• Probably Jossed as of chapter 48, as the mayor clearly turns out to be an incompetent blowhard. If he really were trying to frame the gang, he probably would have had actual evidence planted to take them down, as opposed to the utter lack of it that makes the arrests look moronic.
  • Though it's worth noting that one of the major Crownbreaker spokesponies, Poindexter Heraldry, is the Mayor's assistant.
    • Jossed. He knew Poindexter was involved in the Crownbreakers but thought it was just a harmless social club.

Cotton Mouth's incomplete elixir is the Panacea.

Cotton Mouth himself theorized that the true purpose of the elixir was to push the drinker towards ascension, but the formula was incomplete. Ascension removes the negative (and horrific) effects. What would happen then, if a normal pony took the elixir, and was then hit by Starswirl's spell? It's important to note that, while his incomplete elixir caused massive amounts of Body Horror, he still half-grew wings and his magic did get a boost.

Cotton Mouth only believed he was on to something, but his notes might not be as helpful as could be hoped.

Cotton Mouth's life was pretty much a Shaggy Dog Story; it started going bad and didn't get better. And considering that he is implied to not have been right in the head due to the effects of the faulty elixir on his body, the trauma from his actions, and the abuse under the lich that enslaved him, it's not unlikely his compiled notes could be like a Tome of Madness, with few useful information and mostly insane ramblings. And the author isn't going to make it THAT easy for our heroes to get to the finish line with a shortcut.

Someone from the Alicorn Academy is The Man Behind the Man (and, by extension, the Greater-Scope Villain) of the Crownbreakers.

The Alicorn Academy is the place responsible for creating the "curing disabilities=hate crime" mindset of the Windy City hospital, as well as where the Crownbreakers receive education.

It's very likely someone, who is a "disability normalizing" advocate, does not like the ascension plan, as it will cure disabled people (if Mach's ascension is any indication) and therefore formed and funded the Crownbreakers.

• Partially Jossed. The Ascension plan ISN'T public knowledge, and it's very unlikely someone will try to stop something they know nothing about. Also, if anyone from the academy was responsible, an ambiguous paragraph of someone seething at their plans being ruined would probably have been put in the part where Dash takes down the pretentious scholars of the Alicorn Academy verbally. It's also VERY unlikely that the instigator of the plan stayed to watch the mayhem, specially if said instigator actually knew what the Cloud Solvent Bombs were going to do to the Stadium AND the after effects. There have been absolutely no hints to even point at a potential suspect beyond "There is someone funding the Crownbreakers and we don't know who" basically.

Cloud cities will eventually be legally required to install guardrails or at the very least, have patrols on city edges to prevent accidents.

Since three of the new royals (Fluttershy, Scootaloo and Mach) either had their lives directly threatened by Pegasi negligence or would have been had they lived in a cloud city and Celestia has a deep hatred for ponies who randomly decide "X-group is inferior because [insert asinine reason]", it's entirely possible that cloud cities will be forced to implement safety measures or face consequences (with massive fines that could potentially bankrupt the city/cities in question being the likely minimum and quite possibly having the entire city charged with treason to the crown and having its political chain of command completely dismantled like what happened at Promise).

• Or alternatively, flightless and flight-development-delayed foals will be automatically declared "wards of the crown" and relocated to safe locations. If their parents are willing to come along, fine; if they refuse, tough cookies; they'll have to negotiate for visitation rights which, depending on the child, or the attitude(s) of the parent(s), might be denied. This system could possibly be used as a threat to scare Pegasi politicians into accepting the above since this system would cause their populations to plummet.

Flash Sentry will get ascended.

• Something will happen that will force Twilight to cast Starswirl's spell on her companions and it will ascend Flash. Unfortunately that would mean Luna is out of luck again.
  • To add humor, Flash has a problem with one of his new natures that stems from something like Shining's itty bitty wings. Like maybe he has Unicorn magic surges like a newborn foal instead of the more even keel of the rest of the new Alicorns or his new Earth Pony strength randomly surges, making him trip over his own feet.

Spike will ascend during Twilight's arc, proving that non-ponies can ascend.

• Something will happen that will force Twilight to cast Starswirl's spell on her companions. She expects it to do nothing except maybe give Spike a temporary power boost; however, to everyone's surprise, Spike transforms into the dragon equivalent of an Alicorn, proving beyond a doubt that it is possible to ascend non-ponies. This will prompt some minor testing of the non-pony Nobody's Fools (and possibly Prince Ajax) to see if they have similar qualities to Spike that might enable them to ascend.

Twilight's arc will conclude with a Cthulhu Expy getting utterly demolished by her, Flash, and Spike.

• Hollow Shades is basically Lovecraft Country on steroids, and we've already seen a hint of pony Deep Ones—A (possibly equine) Cthulhu-like being seems a likely antagonist. Who will get beaten down HARD, likely as a Take That! against the "fighting monsters is hopeless" idea of Cosmic Horror.
  • Word of God has confirmed that the Hollow Shades arc will be a Deconstruction of Lovecraft and Cosmic Horror

The Man Behind the Man of the Crownbreakers and whatever is responsible for the state of Hollow Shades are one and the same.

Think about it. If there's an evil Alicorn behind Hollow Shades (as is suggested to Twilight), said Alicorn might have gone mad with power but instead of going the traditional route, said Alicorn retained enough control of their facilities to make a plan to rid Equestria of all other Alicorns and anything else that could stand in their way, with the Crownbreakers and the residents of Hollow Shades as pawns. Of course our evil villain didn't count of one of those Alicorns being Twilight Sparkle and will get utterly demolished by the Power Trio of Twilight, Flash and Spike. Unfortunately, this Alicorn won't be the last antagonist who wants to prevent Celestia's ascension plan, just one of the ones who's the biggest threat.

At some point, one of the new Alicorns will find themselves confronted by a disgruntled non-pony who thinks the ascension plot is a selfish power play (or at least uses that as an excuse for their attack).

Some readers have pointed out some flaws in Celestia's plan, which include but are not limited to "what happens when the land-space runs out?" and "isn't it selfish just to give immortality to ponies?" Naturally, it wouldn't be out of the realm of possibility for a member of a non-pony race to either legitimately believe ponies are selfishly trying to rule the world and try to stop them or just use the reason as a convenient way to make them look noble for attacking the "evil" ponies who want to hoard the secret of immortality for themselves and enslave the rest of the world. Possible candidates include Garble and his crew (especially after RC's excellent use of them in the Nyxverse) or a griffin noble (to serve as a Foil to Prince Ajax). While this plot would ultimately fail, it might force Celestia to reveal more specifics of the ascension plan to the world at large, with the most necessary one being that the ponies are focusing on their own race first to make sure that they know the process inside and out so that it's safe to start trials with other races.

At least one of the underage Alicorns and/or Bishi will be kidnapped by individuals who think the ascension plot is a selfish power play (or at least uses that as an excuse for their attack).

What better way to make "corrupt" royalty listen to you than threatening their children? This will not go well for anyone who tries this no matter who they snatch but they might have the most short-term success if they went after Bishi (since while he's an accomplished martial artist, he's a normal Pegasus otherwise), Mach (since they could grab at least one of the Fools at the same time (or even Scootaloo) and use their safety to make him cooperate) or Jasper (since they could grab Dinky at the same time and again use her safety to make him cooperate). Not that any of the Mane 6, Trixie or Derpy would let them get away with it for long but they might be able to hold the foals long enough to create a genuinely tense arc/mini-arc that ends with Celestia to being forced to reveal more specifics of the ascension plan to the world at large, with the most necessary one being that the ponies are focusing on their own race first to make sure that they know the process inside and out so that it's safe to start trials with other races and that Celestia is trying to make Equestria more democratic.

• For bonus points, in any of the above scenarios, the "helpless" ordinary pony/Fool(s) ends up ascending without any spells required and escapes easily.

There will be a second Windy City arc.

Just like how Neigh Orleans got two arcs (one to introduce the hinkypunks, kappas, and Cotton Mouth, and a second to reveal the source of the former two and bring closure to the latter), Windy City will get a second arc that will reveal The Man Behind the Crownbreakers.

There are two alicorns in Hollow Shades

One is malicious and responsible for all the trouble. The other is the reason why it’s limited to Hollow Shades and why ponies can live there.