The story starts off after Princess Luna gets home from a Nightmare Night celebration. Luna gets some sleep but has a dream where she hears a voice telling her to kill someone. She wakes up abruptly with Princess Celestia sitting next to her. When Luna goes to get a drink of water, she sees Nightmare Moon's reflection in it.

The next morning, Celestia tells Luna to make some friends so she goes off to find Twilight Sparkle, hoping she'll be able to help. When Luna gets to the library, she finds that Twilight is too busy looking for her three missing books which Spike says he loaned to Applejack. Luna then goes off to Sweet Apple Acres to recover the books but Applejack says she only has two of them, and the other, she lent to Fluttershy. As Applejack says this, she mentioned Pinkie Pie's name which causes some reaction in Luna's head, causing her to black out, followed by the same "Kill Her" whispers. When Luna wakes up, she finds out she's been asleep for an entire day.

Without telling Applejack what was going on, Luna left SAA and went to Fluttershy's cottage to get the final book. At first, Fluttershy was scared but after Luna tells her that she just wants the book, she lets her in. Unfortunately, Fluttershy also had to mention Pinkie Pie's name, forcing Luna to go into another coma, hearing those same "Kill Her" whispers. This time, however, it doesn't take Luna long to wake up and finds out that she attacked Fluttershy in her sleep, as she woke up, pinning her to the ground. Again, without any warning of what was going on, Luna grabbed the book and returned to Twilight's library. When Luna gave the books to Twilight, she was about to mention Pinkie Pie but Luna stopped her and told her all the truth. Twilight grabbed a book titled "Possesions" but as she read it, Luna escaped. Twilight grabbed the Elements of Harmony and went to look for the other Mane 6. As she does this, however, Luna finds Pinkie Pie and slashes her in half, thus killing her with all the blood pouring out.

Once the Mane 6 get to that horrible scene, Luna, who now turns out to be Nightmare Moon starts chasing them around Ponyville but trips and falls, making her unconscious. They return to Pinkie's dead body once they see that Nightmare Moon will be out for a while. After lots of crying, they give her a proper burial and leave. At that moment, Nightmare Moon awakens except she's now Luna again. She goes home to the castle at Canterlot and has a talk with Celestia. When Celestia turns around, it reveals that she is in fact not Celestia, and is instead a Zalgo version of Pinkie Pie.

Luna screams in terror and wakes up, now realizing that it was a dream. However, she was in the spot from where she had fallen unconscious as Nightmare Moon earlier. This time, instead of going to the castle, Luna headed for Twilight again who after some qusetioning, decides to help her. They unbury Pinkie's coffin together and see that Pinkie isn't even in it. Then, a Zalgo Pinkamena (with the straight hair, derped and even more bloodier eyes) appears behind them.

Yet again, Luna randomly wakes up, screaming, however in bed in her castle this time. She goes to the main hall to talk with Celestia again but she ends up banishing Luna from Equestria. When she leaves the castle, she falls into a bottomless pit leading into Pony Hell. Looking around, she could see Zalgo Pinkie's and Zalgo Pinkamena's everywhere, forcing her to run as far and fast as she can.

As Luna ran, she fell off a cliff and kept falling until hitting the ground and some grass. She saw shadows of Twilight and Pinkie Pie pass by her but what she wasn't expecting was when she came face to face with Nightmare Moon. They have a conversation, where Nightmare Moon explains that they are the same person. When Luna refuses to believe this, Nightmare Moon forces a crack in the Earth's surface and Luna falls back into Pony Hell once more. There, she sees a normal looking Pinkie Pie but slowly starts bleeding and turns into Zalgo Pinkie who then jumps on and attacks Luna. Luna manages to knock Zalgo Pinkie off her and starts running when she notices now that about 30 Zalgo Pinkie's and Pinkamena's are chasing after her. Eventually, she falls off a cliff and sees the Zalgo Pinkie's and Pinkamena's jump off too. One gets on top of her and Luna closes her eyes after feeling blood drop into it.

When Luna opens her eyes, she notices that the drop was, in fact, not blood, and instead, a rain drop. She was outside in the rain with the Mane 6 surrounding her saying that she fell unconscious while helping Twilight find her books. Pinkie Pie says they should throw her a party and Luna agrees. After the Mane 6 leave, Luna sees Nightmare Moon and has another chat with her. Afterward, she heads to Ponyville and parties with the Mane 6 where Pinkie Pie scares her by putting Zalgo makeup on.

After the story ends, Celestia starts making a "Captains log" which she explains she recovered from the technology of the Starship Enterprise, referencing Joshweiser22's story My Little Trekkie. She also explains how everything was actually not a dream and instead, Luna really did kill Pinkie Pie. Celestia just felt very bad about banning Luna from Equestria so instead, she used Starship Enterprise transporter technology to put Pinkie Pie together and magic to bring her back to life. Then, she erased the memories of all the ponies who witnessed or saw anything to do with the events that transpired. She tries to erase her own memory with her neuralizer (referencing Men In Black and yet another one of Joshweiser22's stories Shaded From The Truth) but decides she just can't do it and is forced to live with the secret from there on out.