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.

In this story, both Dashie and her father remember how it was when they were together. In a process of trying to help them out, Twilight accidentally teleports herself to Dashie's father's world as a filly. After taking care of her for about a week. Celestia and the others come to get her but this time give the option of Dashie's father coming back with her. Everypony looks at the human strange so they ask Discord for help in making him a pony. After tricking Discord, Dashie's father gets turned into a human with a cutie mark of his human version. Then he lives his little Dashie.

Derpy Hooves arrives at Dr. Whooves house after finding a note with the rest of her mail telling her to go there. After introducing herself, Dr. Whooves and Colgate let her in and do the same but in a very mysterious fashion. They explain to her that they're on a top secret mission for Princess Celestia. They want Derpy to help them on their mission but they need to ask for Princess Celestia's permission first.
The three make their way to Princess Celestia in Canterlot. After asking for her permission, she gives it to them, choosing to have faith in her subjects. She explains that their mission is to make sure the changeling threat is gone. Dr. Whooves, Colgate, and Derpy head back to his house and he begins to explain more. The only way to make sure the changeling threat is gone is to follow it from it's source. The source was when they attacked the castle during the Royal Canterlot Wedding. Because of this, they would have to go back in time so Dr. Whooves reveals the TARDIS to Derpy. After an annoyingly painful time trying to explain what the TARDIS was to Derpy, she finally ends up grasping the concept and heading inside of it with the others.

Dr. Whooves then takes the TARDIS to the wedding day and explains to Derpy that she can not tell anypony about the events of the future as it could result in a time paradox causing the very notion of existence to cease to exist. The three get closer to the castle and hear Princess Cadence (who they know to be Queen Chrysalis) singing the first part of This Day Aria. The changelings wouldn't be exposed for some time so they would have to wait, all while not exposing their identities of the future. After waiting awhile, the Queen Chrysalis and the changelings get defeated by Shining Armor and the real Princess Cadence's power. Now seeing their chance, the three head back into the TARDIS and follow them into a changeling colony. After they arrive, Queen Chrysalis looks unhappy to see ponies in her territory but figures she can't do anything about it now. Dr. Whooves makes Colgate and Derpy wait outside while he and Queen Chrysalis head inside a hut. He begins talking to her and his body begins changing, only to reveal that he is actually Queen Chrysalis from the future!

After some explaining, the past Queen Chrysalis joins with the future Queen Chrysalis. Colgate turns out to be one of the changelings from the army and brings Derpy to the dungeon. The two Chrysalises head into the TARDIS and go back to the time when the future Chrysalis first arrived. They managed to rope that Chrysalis in after making that Colgate take that Derpy to the dungeon in the changeling colony as well. As Shining Armor and Cadence were getting ready to defeat the changelings, the three Chrysalises burst in, scaring them for a second causing the spell to fail. Now, with four Chrysalises, they know that even Shining Armor and Cadence's powers can defeat them. The Chrysalises lit up their horns and so did Shining Armor and Cadence. Their power wasn't enough and the Chrysalieses won. All the ponies were laying on the floor.

Meanwhile, right after Colgate took Derpy to the dungeon, someone else appeared inside. It turns out to also be Derpy Hooves. The changeling colony had a protective time bubble on it so that things can go through it but not time. Any time alterations would not effect what happened inside the bubble. The Derpy who got thrown in by the three Chrysalis was there along with the first Derpy. They plotted hwo to escape and did. There was nothing two Derpy Hooves from parallel universes couldn't acomplish. The two ran to where they left the TARDIS and went inside. Now, out of the bubble, things from another universe couldn't exist anymore. Only the Derpy from the alternate universe could. The main Derpy faded away from existence and made sure the other Derpy would eat lots and lots of muffins. Now, this Derpy Hooves would have to defeat the Queen Chrysalises on her own.

The TARDIS suddenly headed for present time on it's own. When she stepped out of it, she was in Dr. Whooves' house again and heard noises from the closet. She found out that these were the real Dr. Whooves and Colgate and that Queen Chrysalis had thrown them in there earlier. They weren't affected by the timeline alteration, though, because his house also had a time bubble. Derpy looked outside and noticed that all the ponies were being used as slaves for the changelings. Dr. Whooves explains that the TARDIS also had it's own time bubble and that's why she wasn't affected either. He goes on a huge speech explaining what she must do to defeat them which is basically to go back in time, use the time bubble as an time explosion, and that should fix any errors made in time. The three risks with that is that she would have to do it before any time jumps were made which means before the Chrysalis Cadence was singing This Day Aria, she would have to go back to the present before the time bubble exploaded or else she would forget all her memory, and once back in the present, she would have to defeat Chrysalis and not get fooled by her again while in Dr. Whooves' form. Dr. Whooves then pulls out a recording device and tells her that he just recorded his whole speech. After time was fixed, he wouldn't remember anything so she would have to give him the recording to listen to. That's when changelings burst in his house and started using their magic against Dr. Whooves and colgate. Derpy ran for the TARDIS with the recording. He heard their screaming of pain and then complete silence, followed by a splatter of red liquid on a window of the TARDIS which she assumes to be their blood and begins crying. Banging on the door by the changelings scare her into place and takes the TARDIS back in time once more.

Once she was at the wedding day again, she realized that Dr. Whooves never told her how to detonate the TARDIS' time bubble. On her own, she comes up with an idea of creating a time paradox within a time bubble which might be enough to make it implode on itself followed by exploding. She finds her own past self and blindfolds her so that no time paradoxes would occur outside of the TARDIS. Otherwise, as Dr. Whooves said, it would result it everything ceasing to exist. Once inside, she takes the blindfold off and talks to her telling her not to do exactly what she was doing now, thus causing a time paradox. The bubble couldn't contain a universe wide paradox and exploded. She sent the TARDIS for the future at the exact same time and fell unconscious. Hopefully she would remember everything when she awoke. If it hadn't worked, even the recording might be lost. Luckily, she awoke all of a sudden but she somehow wasn't in the TARDIS anymore. Instead, she was flying and had a note in her hand to tell her to go to Dr. Whooves house. She had all of her memories and knew exactly what was going on now. She went straight for the house, helped Dr. Whooves and Colgate escape and then tackled Chrysalis in her Dr. Whooves form. She, Colgate, and Dr. Whooves then entered the TARDIS and headed for the Princess' castle. She played the recording for him and then he believed her entirely. They went to talk with Princess Celestia who told them they would need to find the Mane 6 if they had a chance of defeating Chrysalis. They went straight for Twilight's house first and she let them in.

The ponies then went looking for the other 5 of the mane 6. The first they found was Rarity and now she was helping them look. Meanwhile, Spike was still at Twilight's house. He opened the door for who he thought to be Rarity but was actually Chrysalis, as he later found out after she trapped him in Rarity's boutique. She then transformed into Spike and waited for them at Twilight's house. After all the ponies found each other, they headed back to Twilight's house, the location of which Princess Celestia said she would meet them. Once inside, Chrysalis in Spike's form trapped the ponies inside the house and made her way outside to the TARDIS. It wasn't hard for the ponies to escape because they had magic to teleport. They now surrounded the TARDIS and wouldn't let her in. Princess Celestia, Princess Luna, Princess Cadence, and Shinging Armor arrived who Twilight immediately hugged because she hadn't seen them since the wedding now that they were on their honeymoon. They all went inside the TARDIS and used their powers. The power of love, the Princess' power, and the Elements of Harmony. From inside, the power created a chain reaction which cased the time bubble to explode once more except this time it worked as a barrier for the changeling colony. The changelings were now trapped in their colony like a fish in a fish bowl and they had no way out. They had succeeded in finally defeating Queen Chrysalis. After thanking each other, the ponies went back to their homes and Dr. Whooves, Colgate, and Derpy headed back to his house.

Once there, Dr. Whooves told Derpy the full story about how at first he thought Princess Celestia was plotting something beyond the changelings and beyond Equestria. He thought she was planning a conspiracy but now knew he was wrong. He told her also about how he was recruited for Princess Celestia's mission. Afterward, they all went to Princess Celestia to officially make Derpy Hooves a part of their team. Princess Celestia frowned and apologized for what she was about to do but she couldn't have anybody know about anything that could possilby happen. She took out a pen that the three ponies looked into and Celestia used it to make them forget their memories - Men In Black style. She put them in the TARDIS and sent them back. What she didn't know was that Derpy had the recording device recording the entire time and Celestia might had soon be in for it. For now, however, everybody was safe and that was what was important. Even Celestia's secret was safe and if it were up to her, nopony would ever know it...

Meanwhile, as the ponies were partying at Sugar Cube Corner to celebrate Queen Chrysalis' defeat, Spike stayed in Rarity's boutique. Still trapped in the closet. With nopony to help him out.

Electro Spark introduces her immediate family and starts talking about her first years of school of which weren't so good.
She also talks about Dirty McDirtson, her best childhood friend. She was bullied all the time but Dirty was always there for her. Despite one day aquiring his cutie mark before Electro had hers, he continued to stay her friend. Her Grandma, however, was getting a vision of the future. Something terrible was going to happen to Electro, but she didn't know what.

At eight years old, Dirty finally blew his top and was completely jealous of Electro. Due to his young age, he couldn't cope with it and tried to kill Electro in a power plant using electricity but only ended up knocking both of them unconscious. That was when Electro got her cutie mark - a Tesla coil.

After the incident with Dirty, Electro didn't want to stay in Canterlot anymore in order to avoid run-ins with Dirty so instead she moved to Ponyville where she began to make new friends like Shadow Flash, Hunter, and Golden Rod. She also met Kuroi Shiroi and Fire Sparkle along with Hunter's daughter Sheila, and a friend of Hunter's, Slash.

She continues to meet more characters like Light Spark, Sonic Blitz, and Bess who were helping Sheila recover from a sickness. Some ponies named Sparx, Pluto, and Fireblaze were bullying her at the hospital but another pony was trying to help called Snow Eyes. A pony named Tail Sword only made things worse. She found out that Hunter had ponio and it could kill him. Later, she met Mattias Nilsson who also tried to kill her and her friends, along with Derpy Hooves and Pinkie Pie. Her brother Thunder Shock came to visit as well. She also met Jette Black and Plasma bolt who were dating.

After a while of not seeing Shadow Flash, Electro reconnects with him. A pony named Carson was trying to cure Hunter's ponio. She got split into two ponies after she drank a potion that Kuroi made me. She got cider from the first time from Applejack and met Twilight Sparkle. She met Shadow Flame and Fire Heart who were siblings along with Star Swirl who had just opened a new store of which she bought many things using Thunder Shock's money. Another friend of her's, named Titanium Trance opened up a store called Ty's Tunes.

Soon, someone was in Ponyville. It was Dirty McDirtson. After talkign to him a while, she allowed him to apologize and they became friends once more. There were spirits called Aka and Ao who were possesing different ponies but she ran before they could posses her. During hearts and hooves day, there was a lot of commotion with a love potion.

She fought a Hydra with the help of Rai, Free Kick, Blue Thrush, and Sky Dasha, along with Hunter. It turned out fine until she found out that Hunter wasn't actually Sheila's father, he was her brother! They were being mean to each other so she tried electrocuting him, but instead fell off a cliff, fell unconscious, and then fall into a coma.

Five years after the events of the movie Star Trek: Nemesis (Stardate: 61812.5), the enterprise crew is heading towards their rendezvous with Captain Jean-Luc Picard's Ex-Commander, Riker's, ship to create a peace treaty with the Romulans. On the way, however, they discover some turbulence which forces them to crash land on an unknown planet. Once there, they find pieces of Data who got blown up when destroying the Scimitar (events that occurred in Nemesis). When the away team transports back to the ship, Data is somehow all back to normal and fully functional.
In Equestria, Twilight was writing a letter to the princess when Pinkie Pie arrives at her door inviting her to come to Gummy's 2nd birthday party. Twilight accepts and soon the rest of the Mane 6 arrive at Twilight's place. A strange fog comes in and soon an earthquake occurs. Princess Celestia landed near them to warn them that even though they defeated Discord, reminents of his chaos still remained. They couldn't do anything to stop it other than not create any dis-harmony, as it could make it worse, and possibly awaken Discord once more. Immediately, they all go looking for the Cutie Mark Crusaders and find them, arguing, right next to the statue of Discord.

Picard's next step was to promote Data to his new Commander. By sacrificing himself to save him, the Enterprise, and possibly the entire Alpha-Quadrent, made him more human that any of them. Q suddenly appears on the main screen and shows them the ponies and informs them of how they're soon going to meet each other.

As the CMC continued fighting, they accidentally bumped into the statue of Discord, causing it to break his imprisonment and escape. Princess Celestia goes off for the elements of harmony and the Mane 6 fend him off while she does so. To their surprise, they find out that Discord, in fact, is not the one behind the chaos remainding.

Q opens up a wormhole straight in front of the enterprise and starts sucking them in. They tried to navigate away but make no progress. When Princess Celestia return to the ponies, she informs them that a giant wormhole had appeared near the castle in Canterlot and that they would have to investigate. Little by little the Enterprise was heading closer and closer to the wormhole. Once the ponies arrived in Canterlot, they all saw the huge wormhole, and there was a disk-like object sticking out and coming through it. Little by little, it came out and crashed into Celestia's castle.

The ponies ran to the top floor of the castle where the Enterprise had landed. They couldn't see inside but the crew inside could see them. Nothing was making sense for the Enterprise crew. How could they have landed in a world of fictional cartoon ponies!? Rainbow Dash found a way to get in but finds out it's blocked by a glass-looking surface. She gets prepared for a Sonic Rainboom but ends up going even faster after making the Sonic Rainboom after only half way down. By now, most of the Enterprise crew were in sickbay but the bridge crew got into the turbo lift and started heading to the bridge. Meanwhile, the ponies were entering the Enterprise from the outside into the bridge. They looked around when they heard the doors open and saw the humans coming out. After conversing introductions, Q appeared and took Discord with him. Soon, Admiral Janeway contacts Picard and informs him that Benjamin Sisko, who Picard had some relations with (like killing his wife as a Borg called Locutus and introducing him to Deep Space Nine), had been captured and taken to Equestria. Now all that was left was to find him.

After searching in a few locations in Equestria, Janeway contacted Picard again saying that Sisko was in a forest north of where they were. That's when Fluttershy informed them that that happened to be the creepy and spooky Everfree forest. When they arrived there, they met Zecora who led them to where she had found Sisko. Soon Discord appears and tells them that he actually had been spying on Q because no one could create chaos in Equestria except him. He woke Sisko up from his unconscious state and opened a portal to the past. There would be no way to defeat Q now so the only way to do that would be to go back in time and stop the Enterprise from going through the wormhole. Janeway transports there to help them out. Q, however, appears, and makes the portal disappear. Discord makes it reappear and they go off on a series of appearing and disappearing wormholes until one time, their powers collide creating the portal to crack and break, creating a disruption in the space-time continum and they all fall unconscious.

Everyone wakes up somewhere mysterious. They were in Ponyland (the location of which the show My Little Pony Tales takes place) where they meet Starlight and her friends. After discussing how to go back, the unicorns begin using their magic and the Starfleet officers use their phasers at their horns, creating more power large enough to bring them to the present. After going through the portal, however, they find out that they, in fact, did not make it to the present and actually came about five minutes before they left. They find themselves talking to Zecora. Once Q appeared to stop Discord, the future ponies jumped out to stop them from creating a time anomaly. However, by doing so, they themselves create a paradox forcing themselves to be erased from existence and the entire space-time continuum to collapse on itself, causing it to re-expand in the exact same fashion up until the point where it all started: Q.

Pinkie invites Twilight to her party when the others arrive while Picard promoted Data. After the events from the first few chapters happen and Discord awakens, Q decides that maybe it's time he gives them a chance and increases the power of the elements of harmony to seal away Discord for good. Q also gives the Enterprise crew a chance but giving the Romulans an idea for peace. Picard bid farewell to his good friend Riker and the ponies began partying at Pinkie's party. In unison, both Twilight and Picard say "I wonder what adventure awaits us next."