In The Dark Lords Ascendant, a third story in a trilogy of Ranma ½ and Sailor Moon fics known as the Dark Lord saga, Ranma arrives to Juuban to dissuade the Sailor Senshi from thinking that he and the Wrecking Crew are pan-dimensional conquerors (long story, read the first fic to understand where this is going). Of course, this is Ranma we're talking about and the universe seems to hate him for no damn reason, so it goes as well as you think. By this we mean explosions, misunderstandings, and chaos galore. And after the dust settles, Sailor Moon utters these words which shoots down everything Ranma tried to prevent. She's not listing to another word from him, and another fight with the Senshi was now inevitable:
"Are you still going to try and tell us that you aren't mind-controlling these girls into your being your servants, Ranma?"
My Immortal: "Very well [...] Butt we cannot do this. We can’t close the school. There is only one person who is capable of killing Voldemort and she is in the school. And her name is…………………………………………………………………..Enony Dark’ness Dementia Raven Way."
Laughing, Galaxia regarded her opponent. "Oh, I am sure you don't want to join me. Rarely does your kind want to, but they have no choice. You see before this day is over you will be executing the rest the council here and then I think I'll have you kill your own child. After all, I am sure that he is still alive here somewhere and who better to be able to find him than his own mother." Galaxia replied with a wicked smile.
And then the Star Seed is taken by someone else...
In Derelict, Lieutenant Mackie figures out what the SD Nyarlathotep is trying to accomplish after forty-five missions of complete mystery.
Pokemon XD^3: The Waves of Truth: It becomes pretty clear early on that Chapter 21 is a Wham Episode, but you can literally feel the trajectory of the entire story change the moment the doctor tells Rich that Anabel just miscarried twins that he didn't know about.
Blud: "THAT'S WHERE YOUR WRONG MY SHINY HAIRED APPRENTICE. YOU SEE I ONLY PRETENDED TO BE YOUR SHINIGAMI BUT IN FACT I WAS L'S ALL ALONG. I GAVE HIM A LIFE NOTE AND ALL I HAVE TO DO IS WRITE L'S NAME IN IT AND HE WILL COME BACK TO LIFE AS GOOD AS NEW AND YOUR PLANS WILL HAVE BIN FOILLED!"
Chapter 14, after Dark finds some familiar age/sex/location information on a Talk to Dead Dudes Note.
Gordon Freeman: John Freeman you let next boss step on me and made me headcrab zombie. Combines came and put science in me and made me live and strong and big now. I make you and Henry Freeman headcrab zombies. Prepair to die.
Chapter 15: But the realization you’re actually having is that this case is just like all your other cases: a quarrel between a married couple.
Chapter 24: The Sapphire of Alternia is the White King’s Scepter.
A crossover story between Code Geass and Mobile Suit Gundam 00 on the Anime Addventure features this Geass command by Rai on Setsuna for an experiment: "Setsuna F. Seiei, I command you to believe in God!"
When There Was A Tomorrow: We're given the line "For now simply know that your prior feelings when we first met were understandable and I do not think poorly of you for them." Now, what makes this apparent Character Development laden line so surprising? ''''Legion'' is the one saying it! What makes it even Whammier is that when Tali points out this change in behavior Legion insists it's not calling itself "I" and seems genuinely unaware that it's doing so. The exact significance of this line has yet to be seen, however.
“The biggest thing is that there really isn't a curse on Ketafa.”
“It's all been a real game, hasn't it.”
Death Note fanfic Xanatos starts off with L reconsidering his method of catching Kira, and so striking a deal with Rem. We're made to believe that she went along with his plan after L fakes his own death, but then chapter nine gave us this:
Still, maybe she [Rem] was wrong about L...maybe she shouldn't have killed him...
Harry Potter fanfic Pretending to Live has the main Original Character drop this one on a sixteen year old Tom Riddle:
I can help you...with your Horcruxes.
Two in rapid succession at the end of Stars Above Chapter 4:
Nightmare Paradox: It's genuinely hard to say now. I suppose if you were to lay the iterations end-to-end... it'd total a few hundredmillionyears.
Another one comes a little earlier revealing, Paradox is truly Twilight's potential future self. Interesting in that its both a Call Back to Discorded Ponies and one line split between two characters to show how they're the same person.
Nightmare Paradox: I remember wondering if these were the lessons Celestia had intended for us to learn-
Twilight: -and wondered why our coat was turning gray.
From "Bright Eyes part 6": "I am the first born son of Fear and Nothingness." The eldest son of the draconequi, the concept of total freedom through imagination apart from reality, long ago reduced to just a Shadow, makes himself known.
"Shining Armor 13": Cadence proving the Wolf isn't just in Shining Armor's head, and it's still after him.
Cadence: Hey Shining... was there a dog behind you? I could've sworn I saw one when I was coming back down...
From Part 1 of Clover's Gaiden story, we have the meta origin of Pinkie Pie.
Clover/Minty: I…I… don't understand how can this be? ... You were my imaginary friend.
Chapter 7, when Firefly tells her friends why she hates the griffins and why she's upset upon seeing Black Star:
Firefly: Because... he... he...! He killed my parents!
Chapter 16, when Black Star tells Edge to deliver a message for Firefly:
Black Star: (to Edge) I feel regret for killing her parents. Let her know that.
Gilda: So, have you found your reason to fight yet? Dash...
In the popular and acclaimed Avatar: The Last Airbender series Alone: From chapter eleven - "Wait. The Leader can bend two elements?" and "I believe you will have been here four years in two weeks?" The second being a sudden revelation of a Time Skip, akin to a certain scene from The Order of the Stick.
Mai: You see all those years ago, when I got to your letter, something had to be done. You where not sick... like I wanted everyone to believe... I had made something just for you to eat so that little problem would go away... and yes, I took pleaser in doing it...
Hakumei: (extra jarring considering he's essentially leveling a blood feud against his own clan)
Masaru, a.k.a. Arashi no Sasuke/Sasuke Uchiha: Uchiha Yumi...I swear by this blood that I will have my revenge for [Sakura]. Every drop of blood that your spilled will be repaid ten times over. I denounce you, Uchiha Yumi, you and your entire family as hypocrites and murderers. From this day forth, I and my children will never eat with you and yours. I arm myself against you
"This explosion would be seen from several cities away, and it was something that they would never forget. It would also commemorate something else. That day was the day that the 23-year-old gym leader known as Sabrina died.
From The Incipience:
Regigigas: "Ho-oh, it's not a matter of wanting to give you the orb, not that I would give it to you…if I had it."
"'Hmm…how unusual. How did this get here? Interesting. Wonder if this machine is capable of creating this. Will have to see. Interesting prospect, may open new doors. Will have to keep this secret. Ho-oh's shortsighted hatred may make him blind to the possibilities this subject can create,' Uxie said to himself, looking at the single strand of black hair."
Darkrai: "What if we were to remove the dampeners of the humans?"
From The Exigence:
"Butterfree's Protect held for exactly five seconds."
Houndoom: "We mean you no harm."
From The Defervesence:
Uxie: "Muk thrive in areas of waste. Unwanted by humans in cities and unwanted by Pokémon in wild. Coexistence with others in wild difficult due to neighboring Pokémon exhibiting heightened senses of smell. Not uncommon for Muk to be forced into city by aggressive Pokémon in wild. Muk typically forced to live in sewers beneath city to avoid human aggression. Limited light. Limited mobility. Dampener removal and message from you initiated desire to take and expand territory. Despite our eminence, chances of reasoning with them to stop are…low. Will have to eliminate entire species."
Socrates: (on the phone) He's not really doing anything. He's just kinda staring at me. Wait, never mind. Now he's sprinting at me. Sprinting at me very fast... OH MY GOD! NO DON'T DO IT! AAAAAAUGH!
In Part 3:
Socrates: I… I had some psycho with a knife in my house. The guy who tried to kidnap me had a knife.
MTM: Sorry. I mean it. I'm sorry. I genuinely didn't detect him. I swear.
Sighing with relief, Jack got back up again and looked around.
What he saw next almost made him shut down.
It was Dr. Thunderstorm.
In Part 4:
Socrates: This is blasphemy! There's a VHS in here!
In Part 5:
Dr. Thunderstorm: Are they indeed? Well! How fortuitous! We shall have to prepare for them! Not to worry, Frank. I shall succeed where you have failed. I shall destroy Calvin and Hobbes, and I shall use the red-tailed tiger's chip to take over the world!
You don't pay them much attention; most of what little you can gather is wholly transfixed by the round, crystalline pool inlaid in the floor, and by Karkat's unconscious shape floating in it — hair swaying, eyelids translucent, the wide-slit gills lining his ribs gently pulsing in the current.
The Doctor's Doctor: "According to all records, you disappear without a trace on the night of October 12, 2011 - there is no confirmation of you ever showing back up in your proper time period. [...] I. Cannot. Change. That."
The The Avengers fanfic, Brother Avengers: "Actually... you don't know me at all." Spoken by Captain America as he reveals himself to be Loki in disguise.
"Cool!" Calvin said. "But what's down there? It's so dark, I can't see anything. Hey! Cats have night vision, right? Use that!" "Fine," Hobbes said. He looked down, then doubled over and threw up. "What? What is it?" Calvin asked frantically. "See for yourself," Hobbes moaned, clutching his chest. Calvin grabbed a light bulb overtop a stall, extended it, and shone it inside the hole. It was filled with bodies.
"But what does the skull signal mean?" Calvin said. "I'll tell you what it means, Calvin!" came a voice. The duo turned around. Jerome and his cohorts were standing behind them. "It's only the symbol of our cult. It has branches all over the world. We are only this town's branch."
Elizabeth's May 2009 letter: "Said "friend" was a forty year old (she'd just turned the big four-oh April the first) woman named Claire Thompson; when Anthony said she could be my sister, Frank said that was for a good reason: she was!!"
Mike's August 2009 letter: "On the way back, our house sitter called with the news that the Patels filed kidnapping charges on my mother."
Dee's February 2010 ketter: "Mike and I have tried to fight this out, cry it out, pray it out. Saturday, he moved out."
Chapter 7, after the Himes sent back into the three time portals prevent Toki from changing history..
Yukino: "There's a fourth time portal!"
Chapter 18, when Mai decides to ask Meiko some questions about Bachiko, doubting that she has known Bachiko for as long as she thinks she has.
Meiko's expression suddenly darkened, as a feeling of dread overwhelmed her.
They had been found out.
Chapter 18, again when Mai comes face to face with the girl who has been attacking her all this time
Mai: "I should have known it was you... Shiho-chan."
Chapter 22: During a confrontation between Mashiro and the Obsidian Lord.
The Obsidian Lord: "That is incorrect; you are speaking to the Usurper.."
Chapter 24: The Advisor admits to creating the SUEs.
The Advisor: "You have not only triumphed over the rules of the Hime Carnival itself, slain its mastermind and managed to do so with most of you still alive... but you have also defeated several of my most powerful creations."
Magnetism has a flashback to Fluttershy talking to her mom, after school, and at the end the following lines appear:
My mum smiled to this and watched me go without saying a word. It would have been a little scary if she had. After all, photos don’t talk back.
"I had hoped that with medication this would have been taken care of," said Slatt, opening his folder to make another note. Snake fought not to startle at the sudden flash of colour in his slowly blurring vision.
"The hell game are you playing?"
The doctor closed his file. "There is no Hal Emmerich. There never has been."
Olive Branch: I really don't care how you run Equestria. It doesn't matter to me in the end.
Near the end of Families, after Olive Branch and his followers have been dealt with, the story cuts to Garble and his gang, who disappeared from the story after Twilight maimed him, returning to the dragon lands. When they get there, they're greeted by a guard:
Mr. Wily: The city leaders learned about how a NetNavi rebelled on a NetOp so they took advantage of this issue along with Roll's feelings and gave her a mission. That mission... was her betrayal over you by that rare twisted chip.
Dirty Sympathy, when Phoenix is trying to make a joke to Apollo to lighten the mood:
Phoenix: Just how long have you been madly in love with Prosecutor Gavin?
Blue: You know why those scientists wanted to create a powerful pokemon? To fight Pokemon! To fight and kill all of the real Pokemon! You know why the water's polluted. They poisoned it to kill water Pokemon! You want to know who was fighting who, Saylee? Humans were fighting against Pokemon! The enemy was ''us''!
In Armored Gensokyo, A massive fight between Beowulf and Yuugi Hoshiguma has recently ended, and several of the witnesses (and Beowulf himself) are unable to figure out what he is after finally getting him to become sane. And then Reimu has her say in the matter when she hears that Beowulf once died, only to have his body reconstruct itself.
“But not your mind.” [Reimu] said flatly. “You are an Einst, after all.”
In Time Braid, Sakura has found a way for her and Hinata to fuse their time loops with with Naruto's, only for this to happen.