Actions

Work Header

Spy X Family: Case File

Summary:

A spy, assassin, esper, and...a detective? Conan Edogawa ( formerly Shinichi Kudo ) never expected to be suddenly kidnapped and transformed into a child overnight. Desperate for a cure, his search led him to Eden Academy.

Now undercover as a new student, his flawless scores and lack of records made W.I.S.E. suspicious. Twilight was ordered to investigate, uncertain whether or not this mysterious boy will be a threat to Operation Strix.

Meanwhile, Anya thinks he'll be a perfect addition to the family.

Notes:

to be honest—i was lowkey depressed. when i made this, i decided to publish it to AO3 hoping to receive the curse—because sure it's a better substitute than harming one's self, right?

well, im doing better now. still publishing this, so i hope you enjoy!

Chapter Text

Elegant New Student

The old tower bell rang across Eden Academy as a young boy stepped into the gates.

"Find the scientist, find the cure." Conan thought as he adjusted his glasses, scanning the surroundings of the school. The school looked prestigious, neatly paved bricks, black iron gates, even a well crafted statue...but none of it mattered.

The boy was on a mission—faking records and passing the entrance exam to get into Eden was child's play. But the interview nearly blew his cover.

"I have to be more careful, transferring last minute was a risky move, but Eden is the safest place for me to find a way to get that cure. I can't go back to that facility. My best option is to lay low while I find Damian Desmond."

Conan walked through the pathways and slipped inside the halls, careful not to attract any attention. When he finally found the room he was looking for, he took a deep breath before entering.

"Ah, welcome Mr. Edogawa!"

The teacher introduced him as the new transfer student. The students looked at him with interest, some girls eyed him with awe, some girls giggled while some silently began judging him, determining whether or not he has status and connections. As soon as the teacher finished, he told the boy to take a seat.

Conan's eyes scanned for his target as he walked forward. "I need to find that kid, Desmond. He's my ticket to getting close to people who can give me the cure."

His thought perked Anya's interest, she stopped eating her peanuts to give her full attention to the boy.

"He's looking for sy-on boy? What does he mean by cure...is he...sick?" She wondered while he walked towards Damian—to which one of his henchmen stopped him.

"What do you think you're doing? A nobody like you doesn't deserve to sit next to someone as important as Desmond," he scowled.

"Ah, my bad...I was just looking for empty seats! I prefer the ones at the back. I like the quiet," Conan subtly raised his palms defensively, flashing an awkward smile.

He ended up reluctantly sitting on a different table, close to Damian's, but afar from the rest of the students. Anya continued to look at the strange new kid, tuning into his thoughts once more as the teacher started roll call.

"My name is originally Shinichi Kudo. But I'm on the run, so I'm currently using Conan Edogawa—that's the alias I used to forge my records to get in here."

Anya gasped.

"On the run? A fake name?! Is he one of those bad guys on TV?" Her eyes sparkled with thrill.

"—Anya! It's your turn!" Becky whispered.

"Oh—uhh...here!" Anya snapped out of her thoughts, quickly raising her hand before the instructor could bark at her.

As the class went on, Conan listened to the teacher, acting like a good student. Anya, on the other hand, was too busy staring at the kid with interest.

The bell eventually rang. Students started packing up and heading towards the cafeteria. Damian sat with his friends on one of the tables, placing their trays and setting up their meal.

"I have to get close to him," Conan thought, watching him from a distance.

The headmaster suddenly entered the cafeteria. He wore his usual attire, striped gray pants, neatly tied hair, a monocle on his left eye, a cane, and an elegant suit—just like his posture, strict and calm as his eyes scanned around the room for a young boy with round glasses.

When he finally found him sitting alone, he approached his table and spoke in a calm manner. "Excuse me, you must be Conan Edogawa, I assume?"

He began quietly observing his appearance and mannerism, assessing the boy. His eyes sparkled with curiosity but he tried to keep it low-key.

"Those glasses, that haircut—it compliments his face shape...such an elegant look!" He thought.

Conan nodded to his question, to which the headmaster gleamed in delight.

"Wonderful! I have been wondering which student managed to transfer to Eden on such short notice! Would you mind if I join you?" He smiled.

"Of course," Conan smiled back politely, not wanting to seem rude as he tried to figure out who and what this old man wanted.

"How did this child manage to pass the difficult transfer exam test? We normally don't accept transfer students, so we offer a test that's impossible to pass! But he managed to pass it with ease...this child...he's one in a lifetime...HE'S AN ELEGANT GENIUS!!"

The headmaster kept observing Conan before finally speaking, "Ah, I'm afraid I haven't made your acquaintance. How rude of me...my name's Henry Henderson, headmaster and principal of this school." He smiled and held out his hand, urging Conan for a handshake.

Conan shook his hand, giving him another polite expression.

"So, I'm quite curious, Mr. Edogawa. Why did you decide to transfer? Forgive me, if this sounds a bit intrusive..."

"Ah, no—not at all, Mr. Headmaster!" Conan replied and began explaining. The headmaster nodded and listened to him, touched by the boy's calculated words.

"Hmmm...yes, yes...such an interesting student..." He nodded.

As the conversation went on, the headmaster grew thirsty.

"You are quite the special case. Can you care to pass me the tea?" He said calmly.

Conan gracefully poured him a cup, to which the headmaster silently praised him again for his elegance.

"Why, thank you, young man!" The headmaster took a sip and froze—suddenly spitting the tea violently.

"This tea....is NOT—ELEGANT!" He gasped, coughing dramatically.

He grabbed his throat and collapsed gracefully on the floor, causing the teacup to shatter and spill all over the tiles. This caught the immediate attention of all the students in the cafeteria.

"He poisoned the headmaster!" One student stood up and screamed.

"Who? The new kid!?"

Whispers filled the room as gossip began to spread. Conan froze, internally panicking as his eyes widened at the sight of the headmaster dropping to the floor in front of him.

"Poison!?"

Chapter 2

Notes:

thank u to the first guest who left kudos to my work!

altho—im not sure if that was me. i think i probably pressed the subscribe button on accident. but that's different, right?

im going to assume it's a different person. thank you so much btw :D

(See the end of the chapter for more notes.)

Chapter Text

Poison Suspicions

Conan stared at the unconscious headmaster, his face turning blue—the headmaster, not Conan.

"Someone call the nurse! Call the teachers!" A voice yelled out from the room.

Students around him continued to whisper, gossiping about the new kid. Some started to panic, one girl had a horrified look on her face and screamed as she ran out to the hallways.

Conan immediately kneeled down to check the headmaster's pulse—luckily he was still alive, albeit, struggling.

"Let's see...coughing, sudden collapse, shortness of breath...it could be any poison!" Conan cursed.

The teachers and paramedics arrived, carrying the headmaster back to safety as the others instructed the students to return back to their classrooms.

Meanwhile, Conan stood there, still frozen and baffled.

"The tea didn't have any strange appearance or odor. But I need to take a look—"

Another teacher noticed him, pulling him away from the scene. "Kid, you need to come with me."

"No! Wait—" Conan panicked. "I need to analyze the poison and figure out who's behind it—I need to prove my innocence!"

Anya blinked as she watched Conan getting dragged away. "...innocence?"

She jolted, "AH—poisons! I remember my mama talking about it at her job!"

Anya looks around, suspecting no one was watching her.

"Must...get...sample!" She quickly went over to the spilled tea, almost slipping in the process. She bent over and wiped it down with her handkerchief before any teacher noticed what she was doing.

After an intense round of questioning, Conan was released from the office. As he went back inside the classroom, he could still hear whispers and gossip among the students. He was beginning to form a reputation already.

"Aw...nuts! This just made things more difficult!" Conan thought.

"Did he just say nuts?" Anya blinked from her desk, already imagining about peanuts yet again.

"I need to find whoever's behind this and pin it to them. If I keep becoming the center of attention like this...my chances of being found out will be high and they're going to bring me back..."

Conan's mind went into a frenzy of all the possibilities, making Anya dizzy from trying to keep up with his thoughts.

"...I'm a detective, after all. Use your knowledge, Shinichi—what's the point of it if you can't prove your innocence?"

Anya's eyes widened as she tried to hold back a gasp, "a detective!? Waku! Waku!"

"Think, Shinichi. Think! What did I remember earlier?" Conan began replaying his memory from earlier with bullet speed, making Anya impressed but also a little overwhelmed.

"He thinks just like papa..!"

Conan continued to ponder, but eventually sighed. The cafeteria was now off limits for investigation. He couldn't go back to look for clues, and students weren't allowed to leave the classrooms either until the bell rings.

"I should help him..." Anya thought.

As Conan was worrying, Anya decided to walk over to him and gave him her tea stained handkerchief,

"Here," she offered.

Conan blinked, tilting his head in surprise as he tried to figure out what the pink haired girl in front of him was doing.

"Oh—huh? Is this...for me?"

"You look sad, about to cry. Here, take my handkerchief," Anya lied.

Conan hesitated, "Huh? Oh...I'm not—"

"Anya wants to help you!" She insisted.

Conan sighed, knowing he shouldn't seem to be more rude to his classmates now that he already had a bad impression on the class.

He eventually accepted and smiled awkwardly, "Thank you..."

"Why is this stained? This kid better not put her boogers in them..." Conan thought, trying to keep a neutral face.

Anya felt a little offended, but was determined to make her intentions clear by giving him a clue.

"It's stained because I used it to wipe the tea on the floor earlier."

"Huh? Then why are you giving this to me, isn't that unsanitary?" Conan raised a brow, but Anya only stared.

He paused as the realization hit him, "wait, is this the tea that the head master drank earlier?"

"Yes," Anya said bluntly.

Conan felt suspicious. Why would a kid wipe down something that was said to be poisoned? But then again...she looked dumb...it seems like the type kids her age would do.

"I was taught to observe cleanliness but couldn't find a mop...so I used my handkerchief to clean it up," Anya partly lied.

"Ah...I'll keep that in mind, then..." Conan smiled awkwardly. He held the handkerchief with caution, making sure his fingers were only touching the dry part.

"Thanks to this dirty girl, I managed to get a crucial clue."

"Hehe...I'm helping!" Anya grinned, ignoring Conan's insult.

After classes, Conan snuck into the school laboratory. He set out the necessary tools and equipment to investigate the tea.

He pulled out a ziploc bag containing Anya's soaked handkerchief. Conan carefully wrung it, extracting the liquid and pouring it into a vial.

"Let's see..." Conan began analyzing the liquid.

 

"No strange smell. If it were poison like Cyanide or Belladonna, there would have been a distinct almond odor...none of that here. It smells just like what a normal tea is supposed to smell—a mix of herbs, florals like the elderflower, which could be used to mask certain compounds, and...peanuts?"

Conan blinked, confused as to why someone would put peanuts on the tea...

"Who puts peanuts on tea? The headmaster could be allergic to that—"

Conan shook his head.

"No, wait—it's probably from that strange girl...I saw her munching on peanuts earlier when I walked into class. Her crumbs must've been mixed into the tea sample when she wiped it using her handkerchief."

He continued to list all possibilities. Meanwhile, Anya was outside, peeping through the cracked door while listening to his thoughts.

"A detective in the work! Is he like papa? He looks so cool!"

Conan continued his work, "Hmm...no traces of any strange chemicals. The substance looks normal...it just seems like normal tea—no strange anomaly..."

"He's not getting any leads..." Anya sighed, slumping against the wall as she watched other students pass by.

"Waah! This is my fault! I poisoned the headmaster!!" Anya overheard a girl's thoughts.

"WHAT?!" Anya turned around.

"Why did I slip that potion onto that tea?! If anyone finds out I'll be in big trouble!"

"Wah—potion?! Is she...a WITCH?" Anya gasped, standing up.

"NO ONE MUST KNOW!"

"Witch witch witch witch! This is so exciting!!" Anya quickly followed the girl, abandoning the young detective alone in the laboratory.

Notes:

update on previous note: yeah, it was a different person.

Chapter 3

Notes:

(See the end of the chapter for notes.)

Chapter Text

Keep An Eye

Anya trudged through the door, defeated. The girl she was chasing earlier ran too fast for her stubby little legs to keep up. Her suspect got away.

"I'm home..." Anya mumbled, taking off her shoes as Bond ran through the living room, wagging his tail to greet her.

"Bond!" Anya chuckled as the dog began licking her, it was a nice distraction from her current mood.

"Hey, how was school, Anya? You seemed like you had a long day," Yor smiled as she chopped vegetables from the kitchen.

"Not good," Anya replied, leaning on Bond to rest.

"Oh, why is that?" She tilted her head, a hint of worry and curiosity showed on her face.

"Well, there was this new kid at school today, and now he's being suspected of poisoning the headmaster—"

Yor almost dropped her knife, while Loid spat out his drink.

"Ehh? Poisoned? That's a clean way to kill... certainly not my main medium. I mostly prefer blades...haha—but some of my co-workers prefer poisons, I'm immune to poisons, but the headmaster isn't—" Yor rambled in her thoughts, aggressively dicing the carrots that made Bond flinch.

"The headmaster is fine. They took him to the hospital and he's currently recovering."

"Ah, is that so?" Loid took a sip of his coffee before setting it down, completely ignoring Yor dismembering the vegetables.

"This is bad. I had intel that there was a transfer student at Eden, I was too preoccupied I didn't look further into it. You made a mistake, Twilight—you underestimated a child and now there's a possibility of a potential assassination because of him."

"Oh, and who was the transfer student?" He asked calmly, masking his worry.

"Shini—Conan. Conan Edogawa...the new boy from our class."

"Conan Edogawa?" "I'll have to look into him later. For now, all I know is that he's a transfer student in Anya's class, so they're around the same age. Could he be a puppet from a rebel group? Are they trying to use a child to operate their plans and promote widespread panic? Disgusting. But why Eden, out of all places?!"

"Yes, he's the boy with big round glasses," Anya gestured, circling her fingers infront of her eyes to mimic glasses.

Loid nodded, "I see. Do you believe he's innocent?"

Anya nodded back and Loid could only smile.

"Should I contact W.I.S.E. about this? No. I'm sure they're already informed about the incident, but I'll still have to report back to headquarters for any additional information. If he's Anya's classmate, I need to know whether or not he's a threat to the school, and possibly Operation Strix. Could he be after Desmond as well? No, don't jump into conclusions yet, Twilight."

"I-I don't think he's a bad guy! I believe he's a smart and kind kid!"

"Of course, Anya," Loid smiled softly, patting her head to soothe her.

Meanwhile, Yor was still wondering about poisons.

"Say, Anya-san. Why did they suspect the new boy poisoned the headmaster?"

"Well, he was talking to the headmaster and he poured his tea."

"Oh? And what happened after that?" "What were the symptoms? Seizure? Nausea? Vomiting?" Yor started visualizing the headmaster experiencing certain levels of pain and symptoms.

"He just coughed dramatically and fainted," Anya replied bluntly.

"That's typical for the headmaster," Loid thought.

"Perhaps we should pay him a visit then, just to hope for his recovery," he suggested, already thinking of ways to gather intel.

"An old man—I mean, the headmaster is in the hospital but papa is always thinking of work..."

"Oh, we should buy him flowers!" Yor suggested.

Loid smiled, "that sounds like a great idea, Yor!"

"Let's see, what flowers should I buy for the headmaster?" He began formulating different bouquet and flower combinations for their visit.

"A spy must know the arts. Knowing the language of flowers will certainly leave a good impression, as well as to prevent any misunderstanding or rude gestures. For example, white lilies are typically used in funerals. We don't want to send the wrong the message..."

"...as an assassin, as long as we don't buy any poisonous flowers such as Night Shade, Oleander, Fox Gloves..." Yor trailed off.

The husband and wife continued to ponder and got lost in their own thoughts, making their daughter shocked.

"Ehhh? Even flowers can kill people?!" Anya was impressed but overwhelmed with the knowledge that there were dangerous flowers, as well as flowers that could be considered rude to gift someone on certain occasions.

She then excused herself, wanting to go to bed early rather than listen to their thoughts longer.

Later that night, Anya laid in bed, staring at the ceiling. She clutched her chimera plushie for comfort as she slowly began to feel sleepy.

"Conan doesn't seem like a bad guy..." She thought.

"But maybe I should spy on him...for world peace..." Anya mumbled, drifting off to sleep.

Meanwhile, Loid was already at headquarters. He walked through the halls and entered the room to the Handler's office.

"Twilight, good to see you," The lady in red hair smiled, handing him a file.

Twilight took the file and began analyzing its contents.

"Edogawa Conan...a young orphan boy from Westalis. There's a lot missing from his files. I'm counting on you to observe him. I'm sure you're already aware of the poisoning incident centering around him. Investigate that as well. It shouldn't be a problem for you."

"Understood."

"While it's unlikely a young boy would dare to poison the headmaster, we suspect another party was involved. Our men are currently looking into it."

Twilight nodded, continuing to read the contents of Conan's file. No birth certificate, no prior schools, surprisingly advanced intellect, no family records—

"How on earth did he manage to get into Eden?" Twilight thought, sifting through the files until he managed to find his fake records.

"Now I really need to see this Conan Edogawa for myself."

Notes:

btw—requests and corrections are welcome!

i tend to be passionate when it comes to grammar, but my brain can't help missing a few errors here and there. i'd appreciate any corrections involving misspelling, punctuations, etc.

im also not really plotting ahead most of the time, so the future plot of this fic is flexible—depending on what I feel like writing. if you have any requests or suggestions, feel free to comment it.

thank you again, for supporting my work. I'll try to post at least one chapter every week—if that's possible.

Chapter 4

Notes:

okay...yesterday i said I'll try to update "once" a week, but that's like the minimum—

(See the end of the chapter for more notes.)

Chapter Text

Hospital Visit

The next day, the family decided to visit the headmaster at the hospital. Anya was assigned to carry flowers, a bouquet of simple lavenders. It smelled nice, contrasting the clinical air around them.

"Papa, are we there yet?"

"We just need to turn left and walk a few more steps," Loid replied calmly.

When they finally stopped at the room number they were looking for, Loid pushed open the door.

They were greeted with a warm scent. The room was well lit, windows open as the sun beamed through. At the corner, the headmaster sat in bed, staring at the outside. Around him were flowers the previous guests left. He was wearing a simple hospital gown, quite different from his usual formal attire. He looked more relaxed this way. When he heard the door open, his head turned slowly and smiled.

"Ah, Mr. and Mrs. Forger! It's good to see you," he greeted, gesturing for them to come inside.

"I hope our visit isn't interrupting you," Loid smiled.

"Oh, not at all, Mr. Forger! Please, you're more than welcome to stay. Would you care to join us for some tea?"

"Us?" Yor blinked.

"Ah, yes. I sent Conan earlier to fetch me some tea—oh, and you can put those there," he gestured to Anya over the pile of flowers next to his bed.

Anya nodded, walking over to place the flowers while Loid stiffened slightly when he heard the boy's name. "Conan?" he asked.

"—headmaster, I changed the tea as you requested, no more elderflowers since you're allergic..." Conan called out, entering the room carrying a tray.

"Ah, yes. Thank you kindly, young man," The headmaster smiled.

"So this is him." Loid's eyes narrowed.

"We were just talking about you. Mr. Edogawa, these are the Forgers. Forgers, this is Mr. Edogawa, our brilliant young transfer student," he introduced.

Loid stared at the boy while he greeted politely before pouring the tea at the table beside the headmaster.

"Conan Edogawa. I've read your files. What the headmaster essentially said is true, passing the entrance test like that with flying colors...it's no doubt this kid is smart..."

"Oohh! He's a genius detective? And papa's analyzing him!"

"...but to think that this kid managed to get into Eden without any parents or connections—"

Anya overheard Loid's thought, "he's an orphan...like me?"

Loid looked at him, Conan noticed his gaze. There was a silent stare down between the two.

"He seems harmless, but looks are never a solid way to determine someone's intentions,"

"Why is this man staring at me like that?" Conan tried to ignore him, turning his direction to Anya. He relaxed a bit when he recognized her familiar face.

"Oh, hey. It's you." "The peanut girl."

"Waah! How did he know I like those!?"

"That smell spooked me last night. Who puts peanuts in tea? Then I realized… crumbs from her handkerchief when she picked up the evidence...that's probably why." Conan sighed internally.

"Oh."

"Still, why did this kid hand me evidence? It's almost as if she knew..."

"Excuse me, but do you know this boy, Anya?" Loid piped in. While he was suspicious of Conan, there was something else mixed in his worries.

"Yeah, we're classmates!"

Conan nodded along, taking a mental note of the new information. "Anya, so that's her name."

"Why is Anya being friends with a potential killer!?" Yor looked at Conan with a murderous look. "I can't have this little boy being close to Anya! If he does something to her, then—"

Conan tried not to shiver as he noticed another set of eyes observing him like daggers, "Haha, yeah...every kid's parents stared at me like that since this morning. But this couple...why do they seem more intense..."

Anya read their thoughts. Feeling worried that Conan was becoming the subject of her parents' hostile suspicions, she decided to change the subject.

"So...have you proved your innocence, yet?"

Conan blinked at her question, "Ah, no—not yet. But they couldn't prove I was the one that did it either..."

"Although, everyone assumes I was the one who did it. I can't change the opinions of scared students. I just hope this would be all over soon."

"I trust Mr. Edogawa," The headmaster spoke. "While he's a new student, I believe he has no ill intentions towards me or the school."

Loid could only nod, "I agree with you, headmaster." "I don't."

"Papa, you're such a liar..."

The headmaster sighed. "Still, it pains me that your reputation is being questioned, Mr. Edogawa. And worse, with the dormitory situation, I imagine this must be very troubling for you..."

Conan’s shoulders stiffened, but he forced a calm smile. "I’ll manage somehow."

"I can always sneak into the library, or try my luck into the streets again like the past few days before I got accepted to Eden—oe I can try the orphanage again..." Conan began formulating plans to survive.

Anya's heart sank as she read his thoughts. He had similar circumstances before, like her... She tilted her head, eyes darting between Conan and her parents. Suddenly, an idea formed in her head.

"How about staying in our house?"

"Huh?" Conan blinked at her sudden suggestion.

Yor's eyes widened, "WHAT!? Anya-san wants to live with this boy? No, no—She's too young!!"

"Way to go, Anya. I can keep a closer eye on him that way!" Loid thought proudly.

The headmaster seemed to consider the idea. "That might not be such a bad solution. After the recent…incident, I’m afraid the dormitory might take a while to unsuspend your boarding rights, Mr. Edogawa. At least until the matter is settled."

Conan froze. "For a while? So they’re really treating me like a suspect. This is worse than I thought."

"Of course, we can arrange temporary lodging through the orphanage system. I can certainly make sure to cater to any additional needs. But for now..."

"We’ll take him," Loid cut in smoothly, smiling in his usual calm manner. "It would be good for Anya to have a classmate nearby. And besides, our home has plenty of space."

Yor whipped her head towards him, "Loid?! B-but—"

"Yay!! A new roommate!" Anya jumped, probably remembering in the back of her head that their household doesn't have that much space—at least, according to Becky during her first visit. But it doesn't matter.

"I can't waste an opportunity like this..."

Conan forced a polite smile, but his mind was already racing. "Great. Just what I needed… being monitored under the same roof as this suspicious family. But if I refuse now, I’ll draw even more attention…"

Notes:

P.S.

i tend to be a perfectionist. so i might go back to correct the grammar and change the text on previous chapters. maybe alter a few sentences here and there.

so, if you think there's a plot hole, there's a good chance i probably altered the previous chapters to aid said plot hole.