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Apocalypse How: Class 3. Excluding the protagonist, ponies have gone extinct.
Bald of Awesome: Sort of... For survival purposes, the Protagonist shaved of her mane and tail hair off, but some of it remains. In later chapters, it's slowly starting to grow back.
Bittersweet Ending: Multiple times. The time travel arcs have well-earned and cathartic happy endings, especially the Fluttershy and Dredgemane ones. Then you remember that Everyone Dies a few months later anyway.
Broken Bird: The protagonist. Years of living in the Wastes have jaded her, and even her life before that, as a homeless orphan in Ponyville was tough. On the other hoof...
Broken Ace: Years of living in the Wastes have also given her a large repertoire of abilities, such as her engineering skills.
Call Back: In the first chapter of the story, the Last Pony is seen hunting a Phoenix in order to harness its natural flame. The bird in question is sent into a frenzy from her attempts, and in its delirium, nearly kills her a few times. Twenty chapters into the story, she has a flashback where Fluttershy tells her that it's a bad idea to anger a phoenix. She replies with a good-spirited "I'll be sure to never do that."
The End of the World as We Know It: Referred to as "the Cataclysm"; discovering how it happened drives the plot from Chapter 5 onward. As of Chapter 30, the Cataclysm may also be called (or have something to do with an event called) the "Onyx Eclipse".
Late-Arrival Spoiler: The description of the fanfic implied that time travel is involved in the story, but that doesn't come into play for the first few chapters. Other than that, the protagonist is Scootaloo and therefore a pegasus, and the "old companion" of hers mentioned in the description is Spike.
Lightning Bruiser/Nigh-Invulnerability: Harmony, due to her borrowing a part of the power of Entropa, has more than enough Strength to buck over a healthy tree without even trying, and also resilient enough to Tank an entire horde of Trolls for several hours until the Sun rose up and still be alive and well, as well as eaten by a Hydra and go... ALL the way through... And be none the worse for wear. However, while she's certainly capable of taking a lot of punishment, there's only so much otherwise-fatal damage she can tank until the Magic anchoring her to the Past starts to fade, which can fling her back to the Present.
Mystical Plague: Infernite Poisoning, contracted by in contact with the dead god Consus' blood dried blood, and is incurable. until Harmony came in.
Non-Indicative Title: The titles of chapters 31-52 (the Pinkie Pie/Dredgemane arc) are all references to the titles of films, books, and episodes of television shows, edited to include "Pinkie", "Pink", "Pinkamena" and/or "Pie". Any relation between these references and the contents of the chapters is not immediately obvious (with some exceptions, such as "The Moon is Hollow and I have Touched the Pie").
Older and Wiser: Spike, thanks to his experiments with time travel, is 300 years older than in canon, even though only 25 years are stated to have passed since the time of the show. He serves as a mentor and ally to Scootaloo, and provides the means of her time travel.