Months later, Celestia still has Starswirl's journal locked up in a drawer in her bedroom. Luna occasionally asks her about it, but Celestia is never entirely sure how to respond. True, it would mean so much if she could somehow keep Twilight around... but, at the same time, the thought of subjecting her to the same sort of pain that Celestia herself has suffered...
And so, the journal remains in the drawer.
Celestia mentions something odd that has been happening about this time. Her monster hunters, as always, are seeking out and destroying Changeling hives--but, for some reason, they've been finding more and more empty caves, with no sign of the Changelings themselves. They take this as a good sign--the Changelings must be dying out on their own!--but Celestia isn't convinced.
In any case, Celestia prides herself on her Changeling-sniffing abilities. She's gotten very good at telling a Changeling from a regular pony, and has even begun to take notes of the tics she notices. However, she's still more than a little paranoid--and who wouldn't be, after all that has happened to her?
Eventually, Cadance formally announces her engagement to Shining Armor, and soon they've picked a wedding date. Preparations are soon underway, though Cadance seems determined to make them all on her own--she refuses the help of either Luna or Celestia, on multiple occasions. Celestia notices that she's beginning to behave a little oddly, but chalks it up to wedding-stress.
About two weeks before the wedding, Celestia is working in her office when there's a knock at the door. Without looking up, she tells the knocker to come in, and hears the door open and close. She glances up--then leaps from her chair.
Standing in front of her is none other than Starswirl the Bearded.
But--as she continues to look--she notices that something is odd. For one, the Starswirl in front of her is earth pony, not a unicorn. And his coat is a flat white, with crystal-like designs apparently painted on. Celestia begins to grow angry--until there's a flash of purple light, and Celestia is standing, face-to-face, with a Changeling.
The Changeling is a purple one, with neither horn nor wings. Before Celestia can react, the Changeling speaks, in broken English, saying it has a warning for her. Despite appearances, the Oriax hive (the one that captured Cadance) was not driven to extinction. Lately, they've been consolidating power, including attacking other Changeling hives (an inexcusable sin in Changeling culture). The various Queens believe that the Oriax are preparing to make a move against Equestria, though they can't say where or when.
Celestia recieves this information in silence. When the Changeling is finished, she asks why he is telling her this. The Changeling looks away, and reveals that Celestia has a reputation amongst Changelings--a reputation as an apocalyptic force, one that, if she had her way, would scour all the Changelings off the face of the earth. Though several hives are inclined to leave Equestria to its fate--thinking, perhaps, that the Oriax might even be able to bring down the Pony-Queen--this Changeling's Queen, over the objections of her hive, asked him to relay this message. She is doing so in the hope that Celestia will, perhaps, begin to see reason, and may, eventually, leave the Changelings alone.
Celestia is silent for several moments, before, quietly, telling the Changeling that she will not change her decrees: that Changelings are forbidden in Equestrian territory, and are to be killed on sight. The Changeling turns to go, but Celestia adds that, since he has done her a service, she will give him twelve hours to get him, and anyone he cares about, out of Canterlot. Beyond that time, there will be no mercy. The Changeling hurriedly bows and backs away--but not before Celestia commands him to choose a form other than Starswirl as he leaves.
Celestia immediately begins to make arrangements to keep Canterlot safe and Changeling-free, including recruiting Shining Armor to use his special talent to throw up a city-wide shield (though she begs him to let other unicorns help out). Four hours after meeting the Changeling, Celestia is urgently summoned to the courtyard, where she finds his mangled body surrounded by guards. He had been found, minutes before, hung from a palace spire by his lower jaw. Celestia thinks she should feel something--perhaps a sense of sadness at the savagery shown in the killing--but all she feels is a sort of vindication. Serves him right... though she's at a loss to explain what or why.
The day of the wedding approaches, and Celestia has been scanning the guests for signs of Changelings. Twilight and friends show up, though Celestia isn't able to pull herself away from the proceedings long enough to spend the time with them that she would like.
That night is the wedding rehearsal. Things are going smoothly, and Celestia is about to allow herself to relax, when Twilight bursts in. She is obviously hurt and angry, and accuses Cadance of being... something else. Everypony gets angry with her, with Cadance subtly egging them on with tales of how mean Twilight has been to her. Celestia watches the proceedings in silence.
Suddenly, Celestia steps forward, and, in a voice that silences the others, begins to tear Twilight apart. "How dare you try to bring your jealousy into their happiness." Twilight begins to cry, but Celestia persists: "I expect better of my students. I think it's time we have another chat about your continued enrollment in my school. Go to my office. Now." Everyone, except possibly Cadance, is horrified by this turn of events.
Celestia leads a weeping Twilight to her office in silence. As soon as they're inside, Celestia closes and locks the door, and Twilight begins to plead with her. However, Celestia spins around and hisses, urgently, for her to shut up.
Twilight is shocked into silence. Celestia calms herself, then asks Twilight a super-personal question ( 
"On your first day of school, you wandered into my office. Why?" 
"I, um... what?" "Twilight, I mean it. Why?" "I, um... I h-had to go to the bathroom, and I got lost..." "Good."). Celestia asks her to ask a similarly-personal question, one that only the two of them would know. Twilight, nervous, flubs it, but Celestia lets it slide ( "Uh... w-what's your favorite flavor of ice cream?" *eyeroll* "Strawberry.")
Twilight, confused and afraid, starts to get emotional again, but Celestia shuts her up by revealing that she believes her. Twilight, eyes wide, watches as Celestia begins to poke around the corners of her office, looking for hidden lurkers. As she does, Celestia confesses that she expected something like this--though she never expected Cadance would be the infiltrator. Whoever is impersonating her is doing a very, very good job--very nearly good enough to fool her, in fact. When Twilight made her accusation, all the pieces fell into place, and, now that she knows who her enemy is, she can begin to fight her.
Celestia turns to Twilight and tells her that, first, she must go back and apologize to not-Cadance. If they're going to have a chance at all, she must believe that they don't suspect her in the slightest. After all that is done, she is to gather her friends and take the next train to Ponyville. When they get there, they are to go to the Tree of Harmony (where they have been storing the Elements since the fight with Discord), retrieve the Elements, and return here as soon as they can. Twilight does some quick math, and points out that, if they follow that schedule, they will make it back to Canterlot after the wedding itself has taken place. Celestia hesitates (admitting, to her listeners, that that was the entire point), but insists that Twilight do as she asks.
Twilight asks Celestia what she's going to do. Celestia is going to call in every favor she has--this Changeling has to be brought down, and she has no idea what tricks she might have up her sleeve. She's not going to make a move until she has all her ducks in a row--jumping the gun could result in even more deaths. Twilight asks, anxiously, about her brother, and Celestia swears to her that she will do everything in her power to protect him.
Celestia sends her off, then locks herself in her office and begins to frantically write letters, pitching them into the fire as quickly as she can get them out. A short while later, she sends a note, asking that Shining Armor stand guard outside her door, ostensibly to indulge her old-mare paranoia; in reality, she's doing what she can to keep him away from Not-Cadance.
Celestia stays up that entire night rallying her forces, kept awake by her fear and anxiety. However, part of her is able to rest easy, knowing that Twilight and her friends are safe.
The next morning, Celestia emerges from her office, feeling much better about things. However, she almost immediately runs into Pinkie Pie, prancing down the hallway. Stunned, she asks Pinkie why she's back so early; Pinkie reveals that they never left, and that she hasn't seen Twilight since the rehearsal last night.
Celestia is deeply frightened, but decides to press onward as if nothing is wrong. After all, help is coming, from all corners of Equestria, and all she needs to do is wait.
Celestia puts on a good face, and manages to make it to the wedding itself without, she thinks, not-Cadance suspecting a thing. She doesn't listen to the ceremony, preoccupied with other things. She has no idea who not-Cadance is, nor what she's planning--but, as soon as she finds out, she's going to annihilate her and everything she cares for. Celestia is also worried for Cadance herself, but convinces herself that she can only worry about one thing at a time, and the only logical thing for her to do is eliminate the threat. But not yet. She has to wait. If her time playing chess with Starswirl taught her anything, it was that patience is how you win the game. Wait, watch, and, when you have all your pieces in place, strike. That's the way--
At that moment, the doors to the chapel are flung wide. Celestia, with the rest of the crowd, turns to stare--and they all see a ragged Twilight Sparkle, at the side of a scrawny, dirty, and wounded Princess Cadance.
Celestia's eyes grow wide. Goddamn it, Twilight, she mouths.