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The Scent of Mystery

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The Scent of Mystery: Chapter 1.


A yaoi Detective Conan Alpha/Omega A/U.

Notes; Shinichi and Ran are Alphas. Ran knows Shinichi is Conan because Alphas have a good sense of smell and she was able to recognize Shinichi's scent coming from "Conan" when they met after his body shrank. Kogoro Mouri is still clueless about Conan/Shinichi helping him. Ran and Shinichi are Just Friends.


Shinichi/Conan was reading the newspaper in the office of the Detective Agency his Ran's dad, Kogoro Mori.

It's been over a year since Kudo Shinichi was shrunk into a kid by the Black Organization, and there wasn't a single real lead on them. Although he did acquire a former Black Organization scientist as an ally, who also took the same drug as him, her alias is Haibara Ai (a Beta). She was currently working on a cure for the drug.

And so far, Shinichi had been, somewhat, able to re-adjust to being back in an elementary school. Under normal circumstances, he would've been able to blend in easily (despite acting like a child was hard for a brilliant teenager like him), but Shinichi was an Alpha and unfortunately, his Alpha statues did not go dormant when his body shrunk to the size of a seven-year-old (8 currently). Since the Sub-Sex normally surfaces during puberty (between 12-14 in this world), "Conan" had a bit of a problem. Fortunately, Agasa-hakase (1) managed to explain to the staff at Teitan Elementary School that "Conan" was simply an early bloomer and was able to control his pheromones pretty well.

Shinichi/Conan sighed and thought 'It's been one crazy year.' He really hoped Haibara could come up with a cure for the drug soon, or that he could take down the Black Organization. Either or.

"Smoke's coming out of your ears," Ran said over the couch where Shinichi/Conan sat. The teen turned boy looked up to see his childhood friend looking down at him. "Oh, Ran, I didn't hear you come in," the teen in a child's body said as he folded the newspaper. “You’re thinking too hard again,” Ran stated with a giggle. Shinichi/Conan sighed and finally noticed that Haibara was there too.

"You're thinking about the Black Organization, aren't you," Haibara stated rather than asked. Shinichi's/Conan's eyebrow twitched at that and wondered if Haibara had some kind of sixth sense about these kinds of things.

The sandy blond pointed a finger at the teenager-in-a-child's-body and stated "I've told you hundreds of times to not think about That Organization. It's bad for you to do so." Ran agreed with Haibara when she said: "It'll ruin your ability to focus on a regular stuff."

Shinichi sighed a bit. He knew they meant well, Ran more than Haibara, but even though they knew how he felt about the Black Organization, they didn't really understand how he felt.

<> One Week Later <>

The Detective Boys were currently doing their "Helpful Civilians" assignment that Teitan Elementary School did to promote goodwill to their students. They were volunteering at the Omega Clinic that Dr. Adaide worked at on the weekends. Ran came with them as their sponsors for the Helpful Civilians program.

Ran and Shinichi/Conan had to wear masks because of their heightened sense of smell, and Omega pheromones are strong to Alphas.

Dr. Adaide was really grateful for the help, especially Ran's. Since most of the Omegas that were admitted to the Omega Clinic were abuse cases, mostly by older Alphas, and having a younger and gentle Alpha actually helping out at the clinic would be good for the mental healing (Ran, of course, can't actually be next to any of the Omegas, but having her being seen helping out works just as well).

Genta and Mitsuhiko pretty much got on Conan's case about not being a bad Alpha who hurts Omegas when he gets older. "Oh, come on you two! Do you really think I would purposely hurt someone like that?" Shinichi/Conan said with a huff, a bit annoyed that those two would even think such a thing. Shinichi has seen enough of Omegas being mistreated to make him not want to add to that. Even if it WAS Technically Against the Law to abuse an Omega. But it was more of a moral sense not to do it that really stuck in the mind of the young genius detective.

With that Shinichi/Conan decided to go outside, to clear his mind and to take his mask off for a bit. Maybe it was because he was a bit aggravated, or that the mask might have been a bit too thick, but Shinichi was finding it a bit hard to breathe.


Once Shinichi/Conan found a nice garden area on the side of the Omega Clinic, he sat down on the steps, took off his mask and took a deep breath.

"You do know they mean well," Ai told Shinichi as she joined him on the steps. "Yeah, I get that, but it was how they said it that made it sound like they were assuming that I would actually do something like that," Shinichi said with a sigh. Not all Alphas were bad, but all those Omegas with injuries from Alphas... It just makes it hard to get rid of that stigma.

"I can understand their concerns though," Ai said softly, before saying "Gin is an Alpha, a strong Alpha." Shinichi gave a look that said, "Somehow, I'd figure that." Ai took a deep breath and said "Whenever he wanted to make a point, he'd release his pheromones... And... It was.... Very powerful... Even the other Alphas obey when he did that." Shinichi has heard of those kinds of Alphas, but he never thought they were real. And Ai was never one to lie. Keeping certain information to herself, yes. Lieing, no. Shinichi glanced at Ai, who was shaking. It was obvious that what she was about to tell him was a bad memory.

<> Flashback <>

Sherry (Ai's codename during her time at the Black Organization) was walking towards her lab, keeping her routine.

"Why the fucking hell should go along with that plan?" Sherry heard someone close by shouted. She peered around the corner to see what was this fight about.

From what Sherry could tell, a group of Black Organization members were gathered (Gin and Vodka in the group), probably for a mission, and one of those members was obviously not thrilled.

Gin lit a cigarette before saying calmly "The target's an Alpha an will easily be able to smell another Alpha nearby, especially if it's an unknown Alpha. Hence why Chianti will make the shot. She's a Beta and doesn't give off much of a scent." The annoyed BO growled and snapped "But this involves a close shot! Chianti's an amazing sniper, but her close-range shooting's terrible!"

Chianti snapped an "OI!"

Gin gave the annoyed BO a cold look and stated in that same tone "Her close range is fine. She will be able to make the shot in one try without drawing attention to herself, thus completing the mission perfectly. Unlike you." The BO member growled out an "I'm perfectly capable of completing the mission!"

Gin puffed out a bit of smoke before saying "You can't control your phenomenon. You'll give yourself away the moment you take aim." The BO member was furious, releasing his pheromones, and snapped "I can control them just fine!" Sherry wrinkled her nose at the smell, to her it reeked. The others in the group backed away a bit to distance themselves from the aggravated Alpha. Chianti took three steps back while Vodka backed towards Gin, who made no movement.

With a smirk, Gin said "You call that display "Control"?"

A tsunami of a powerful Alpha pheromone washed away the smell that was already in the air.

Everyone just froze, Sherry included.

The scientist could feel the sweat of arousal trickle down her neck and felt the underwear she wore become moist as her womanhood started pulsing. All because of this overwhelming display of pheromones. And it seemed to be coming from Gin.

With a sinister smirk, Gin said "Being able to weld this kind of pheromones is "Control". But compared to yours, I might as well be comparing a newborn kitten to a full-grown tiger."

The once annoyed BO Alpha dropped to his knees, eyes widen, a tent formed in his slacks, and a wet stain formed over his crotch.

"Any more complaints about the plan?" Gin asked, retracting the pheromones a bit.

<> End Flashback <>

'Yikes, Gin's worse than I thought,' Shinichi thought with a shiver.

Shinichi took another deep breath and said: "The flowers here smell nice." It was true, the flowers did have a very pleasant scent. That Ai could agree to.

<> The Next Day <>

The Detective Boy was back at the Omega Clinic, helping out again. There were more Omegas today, about 80% of them were just here for their monthly checkups. That was a big relief for the children. So now they were making sure that all of the doctors had enough supplies for all of the checkups.

Shinichi/Conan went to get some of the small plastic tubes for the blood work when he smelt something sweet. 'Odd? I'm wearing a mask, I shouldn't be able to smell anything,' Shinichi thought as the sweet smell seemed to fill his nostrils. 'Something about this scent just...' Shinichi thought before his mind went blank.


"OI! Conan!" Genta said, looking around for the boy in question. After all, one of the doctors needs more of the tubes for blood, and Conan hasn't returned with them. Mitsuhiko arrived at told Genta that he couldn't find the glasses wearing boy. Ayumi second that motion. Ai and Ran just gave each other a look.

"Are you looking for your little Alpha friend?" An Omega asked the group of children and teenager, before adding "I saw him go in that direction," pointing down the corridor that Conan went down. The Omega then said "He looked a bit dazed as he walked. I'm not sure if his mask was on right, but I think maybe all the pheromones might have been getting to him."

"He still should have said something if he was going out for air," Genta stated, arms folded in annoyance.

For some reason, Ai and Ran weren't sure about that.


Shinichi continued to walk down the corridor, still dazed and still following that sweet scent. He just couldn't resist this scent, he had to follow it! He still had his mind, but his body just followed the smell.

'What's going on? My mask is on right and it's thick enough... So I shouldn't be able to smell anything...' Shinichi thought to himself as his body kept following the smell. The shrunken Alpha then thought 'Is the scent that strong?'

The irritable scent led Shinichi to a closed patient room.

He opened it and walked in. He took a few steps towards the source of the scent.

When Shinichi regain his senses, his eyes widened in shock.

'Why-' Shinichi thought before someone walked in and snapped "What are you doing here?!"


To be continued...


1)) Hakase is basically a Japanese honorific for someone who is a doctor or has a doctorate.

Chapter Text

The Scent of Mystery: Chapter 2


"Conan!" Genta shouted down a hallway.

Dr. Adaide quickly told the chubby boy "Genta-kun, please don't shout. We have patients that are resting." The chubby boy apologized. Mitsuhiko then said, "But Conan went off somewhere without telling us." Ayumi told him that she was starting to get worried.

That was when Genta said, "Conan better not have gone off on a case without us and skipping his Helpful Citizen duty." Mitsuhiko and Ayumi agreed on that.

"Honestly, I leave to get some fresh air for a few minutes and you guys think I went off on a case," Conan stated in an annoyed tone as he walked up to the group, mask back on his face. Everyone turned to the boy.

Dr. Adaide looked over at Conan and said "Well, you did leave rather suddenly. But, I guess that all the pheromones from the Omegas were getting to you, even with the mask." Conan nodded and said, "They were, and sorry for leaving without telling you about it, Sensei."

Dr. Adaide patted Conan on the head and said: "It's alright, but make sure you tell me or one of the staff next time, okay." Conan nodded. And with that, everyone went back to helping out.

Ai and Ran had a feeling that Shinichi/Conan was hiding something.


When it was time to go home, and once it was just the two of them, Ran asked Shinichi what really happened at the Omega Clinic.

Shinichi/Conan was quiet for a bit before he said: "It was just the pheromones getting to me." As much as Ran wanted to push the issue, she knew her friend already seemed conflicted about it and didn't ask about it. She knew he'd tell her when he feels better about it.

<> The Next Day <>

At Teitan Elementary Class 1-B, Conan had a hard time paying attention to any of the lessons. Kobayashi-sensei and the Detective Boys noticed this right off the bat. The teacher asked Conan if he was feeling alright. That was when the teenager-turned-boy said in a tone that indeed made it sound like something wasn't right "Ano, actually, I am feeling a bit under the weather... Is it okay if I go to the nurse's office?"

Kobayashi-sensei nodded and gave Conan the hall pass. He left the room without much as a "goodbye" or "see ya later". Now the Detective Boys KNEW something wasn't right. Ai narrowed her eyes at the doorway.


As Conan/Shinichi walked down the hallway towards the nurse's office, he had a serious look on his face. Dr. Adaide was working at Teitan Elementary today, more specifically, the nurse's office.

A glare of light cast over the glasses the young genius wore. He needed to talk to Dr. Adaide, this was important.

<> <>

"WHAT!? Is this a joke?!" Jodie Starling shouted as she slammed her hands on the meeting table of the FBI's Japanese Branch in both shock and disbelief.

After the news that she, as well as all the other agents, had just heard. Who could blame her for reacting in such a matter?

"From the information, Kir had sent to us, I can assure you that this is no joke," James Black stated seriously. He was in no mood for humor, with all things considered.

Shūichi Akai lit a cigarette and asked: "What else did the information Kir send you say?"


Shinichi/Conan walked into the nurse's office, and as predicted, Dr. Adaide was there. He was sitting in the swivel chair, reading a book.

"Sensei (1)," Conan/Shinichi said, getting the doctor's attention. The doctor looked up from his book, smiled at the boy, and asked "Conan, good to see you again. How are you feeling?"

Shinichi/Conan bit his lip, before looking up at the doctor and saying in a frantic tone "The Omega Clinic is haunted!" Dr. Adaide raised a brow and asked: "Why do you think that the Omega Clinic is haunted?"

Doing his best to act like a scared child, Shinichi/Conan explained it as a child would "Because I got possessed by a ghost! It made me go to one of the patients' room against my will! And it made everything smell really really really nice for some weird reason!" Conan lowered his head and added "I'm sorry for not telling you yesterday, but I didn't want to scare away everyone. The Omegas need the clinic..."

Dr. Adaide placed his book on the table, turned fully to the boy, and asked in a rather serious tone "Did it seem like the smell was going through your mask? Even though it was on correctly?" Conan thought for a bit before saying "Now that I think about it... It didn't. I covered my mask with my hand when I first smelt it, so I thought I was just imagining the smell. At least... Until the ghost took over my body and made me go into one of the patients' room."

Dr. Adaide then asked, "Did it feel like you were being led there by a tugging sensation?" Conan nodded vigorously and said "Yeah! It did! Wait? Did you already know about the ghost, Sensei?"

The doctor placed a hand to his chin and thought for a bit. After what felt like hours, Dr. Adaide asked "Conan... Do you know what a Soul Pairing is?" Conan/Shinichi thought for a bit before saying "Kinda. Ran-neechan (2) told me about it because they teach that stuff in high school. But she figured it would good for me to know since I'm an early bloomer. It's a type of pairing between an Alpha and an Omega, right?"

Dr. Adaide added on to that by saying "Yes, but it's more than that. A Soul Pairing is basically when an Alpha and Omega have an instant link when they meet for the first time. However, neither the Alpha nor Omega will become aware of it immediately, in fact, they will only become aware of that when they are in the same vicinity when they meet a second time and if neither of them are taking any kind of suppressants."

Shinichi/Conan was actually surprised by this when he said "Really? That actually explains why nothing happened when I first met him." Dr. Adaide didn't miss that, especially when he said: "So you met this patient before you volunteered at the Omega Clinic?" Shinichi realized that he slipped up. He had to think up a story, and fast!

Shinichi/Conan looked up at the doctor and said "I ran into him a couple months ago. A little literally... We only interacted for only a few seconds and I didn't get any names..." Shinichi was REALLY hoping the doctor wouldn't ask any more questions. There was no way he could keep up this "Conan" act if the adult realizes that he was older than he currently appears.

Dr. Adaide thought about it for a bit, but to Shinichi, it felt like hours.

"I suppose that makes sense," Dr. Adaide finally said. Shinichi gave a mental sigh of relief at this. The doctor then said, "A lot of these Soul Pairings usually never meet a second time, making them an Incomplete Pair." "Wow, really?" Shinichi asked, doing his best to keep his "Conan" tone. The shrunken teen was glad the doctor didn't ask any more questions.

Dr. Adaide brought a hand to his chin when he said "But in your case, things are a bit different. And a little difficult..." Shinichi/Conan tilted his head, raised a brow, and asked: "What do you mean by that?" The doctor looked down at the teen-turn-boy and asked "Would it be alright if you come to the Omega Clinic today at 17:00? With your parents. This is a pretty big thing." Conan nodded his head and said "I will, but my parents are still out of the country. Is it alright if I bring a close family friend instead?"

Dr. Adaide thought about this for a few seconds before saying it was fine.


Later that day, at 16:30...

"Why the hell are you brats in my office?!" Kogoro snapped at the Detective Boys, who were sitting on the sofas in said office.

Shinichi/Conan knew why, and quite frankly, it annoyed him to no end. 'Damn it. Can't these kids just mind their own business,' Shinichi thought before casting a glance at Ai and thought 'They even roped her into this... Damn it, how am I going to get away from them?'

Yeah... It was pretty obvious that Ginta, Mitsuhiko, and Ayumi knew that Conan was going somewhere today and they thought he was going on a case, so they tagged along, yet again. Shinichi/Conan really hated that, not everything he did would end up in a mystery... Okay, about 90% of the time he ended up in some kind of mystery, but that gave them no right to tag along. They nearly got themselves killed a good number of times because of this careless tag-a-long mentality they had, and every time they failed to learn their lesson.

'I need to think of a way to leave without them following me,' Shinichi/Conan thought, trying not to look suspicious. He needs to get to the Omega Clinic on time and without the kids.

Suddenly, the phone rang.

Kogoro answered the phone and said "Yes, Mori Detective Agency....... Megure-Keibu (3)? ..... Ah, that isn't a problem for the Great Detective Mori Kogoro! I'll be there as soon as possible!" The adult grabbed his jacket and told his daughter "Ran, Megure-Keibu wants you at the station too." The teenage girl nodded and told the kids that they needed to go home.

But, as usual, Genta, Mitsuhiko, and Ayumi didn't listen and dragged Conan and Ai along as they followed the (very annoyed) detective. The only thing Shinichi thought was 'Oh, come on! I really need to meet-' That was when the shrunken teen saw a familiar car as the group walked towards the Police HQ. This gave Shinichi an idea.

As the kids pestered Mori about what case Megure wanted him on, Shinichi slowly lowered his walking pace. Ai chined in an "I doubt that" every time one of the kids said something really out there, like a million billion yen diamond being stolen, which did make Ran giggle a few times.

By the time Shinichi stopped walking, the group was already almost out of sight, not the least bit aware that he wasn't among them. With a sigh of relief, the shrunken teen turned to the street, just as soon as the familiar car pulled up beside him. Shinichi smiled as the passenger door opened.

Shinichi hopped into the car, closed the door, and buckled up.

Now all that's left to do is head on over to the Omega Clinic.

<> <>

By the time they got to the Omega Clinic, Dr. Adaide was waiting outside for Conan/Shinichi.

"Ah, you must be this close family friend of Conan's family," Dr. Adaide said as he shook Shūichi's hand. The FBI agent nodded and said, "I am, and Conan wanted me to come in place of his parents because this is important." The doctor nodded and replied "It is, and I do apologize about not really telling Conan a lot of information... But I believe that it be better to explain it with everyone."

With a soft smile, Shūichi said "I figured since this involves Conan's Soul Pairing, but may I also ask why it would be difficult? I don't think the fact that Conan is a child would be that big a deal." Dr. Adaide shook his head and said: "No, it isn't that." The doctor motioned for Conan and Shūichi to follow him into the clinic. So the two did.

The doctor gave Conan a mask, due to the Clinic's policy. Shūichi took a mask since he was also an Alpha.

They then started walking down one of the hallways of the clinic. A hallway that Shinichi remembers easily. They stopped at a door that the shrunken teen went through not too long ago.

Dr. Adaide lightly knocked on the door. "Who is it?" A voice from the other side of the door asked a few seconds later. A voice Shinichi recognize immediately. "It's Dr. Adaide," the silver-haired man replied in a calm tone. The door then opened slightly, leaving the door open a crack. But it was enough for Shinichi to see the person a bit. "Sensei, is everything alright? You're usually here on the weekends," the voice asked the doctor in a confused tone. Dr. Adaide smiled softly and said, "Oh, everything's fine, but something came up with a volunteer the other day and it involves the two of you."

The owner of the voice opened the door a bit more and said "What are you talking about? I don't remember any volunteer near this room, just a kid I had to kick out." "You mean me?" Conan said in a cheerful tone. The owner of the voice finally noticed the FBI agent and the shrunken teen, and he paled a bit. Dr. Adaide didn't really seem to notice when he said in a tone that was trying to be gentle while breaking a harsh truth "This child was apart of the Helpful Civilians project, and he seems to have noticed a strong "aroma" that drawn him to your chosen bond."

"Chosen Bond?" Shūichi asked with a raised brow. That was when Conan/Shinichi asked in a confused tone "You mean that person you said was my Soul Pairing is already Bonded?" The one inside the room was unusually silent for a good couple of seconds before finally asking "The kid's an Alpha? And is the Soul Pairing to... Is that really true?"

Dr. Adaide, Shūichi, and Shinichi nodded at that as the doctor said "Yes, it is, and this is something I believe that all of you need to hear. Is he awake?" The man glanced back into the room and said "He is now, but... Is this really a good idea, Sensei? He's still not well." Dr. Adaide said in his calming doctor tone "I'm very aware, however, this is important to the both of you. And since it's a Soul Pairing, it might be beneficial for your chosen's health."

The man was quiet again for a bit before adjusting his mask and asked as he turned his attention to Shūichi "And... You're just here because of the kid, right?" Shūichi nodded and said "That is correct. He called me about finding his Soul Pairing and asked me to come because I'm good friends with his family. I have no other reasons for being here."

After what felt like hours, the man cast a quick glance inside the room, then back at the FBI agent and child and said: "Alright, but I'm telling you now, no funny business, I'll kick ya out of here without a second thought if you do." With that, he let them in.

A nurse rushed over and told the doctor he was needed for an emergency incident. Dr. Adaide did ask if it was alright for him to leave without explaining this whole ordeal. "Ah, actually Sensei, I think it might be less awkward if you weren't here," the man said in a bit of a nervous tone. The doctor nodded before letting the nurse led him away.

"You'd better be telling the truth about the brat being the only reason why you're here, FBI dog," the man hissed softly with venom. Shūichi eyed the man and said in a calm tone "I have no reason to lie. But how about we continue talking inside, where we're not going to be overheard, Vodka."

Even though he wore shades and a mask, it was a bit obvious that Vodka was glaring and scowling at the agent. "Fine, but as I said earlier, no funny business," Vodka said, opening the door wider for them to come in. The agent and shrunken teen complied. Once they were in, Vodka closed the door.

"I would also like to say that I would have never thought that this outcome was possible," Shūichi stated with his eyes closed. Vodka brushed by the agent in a not so gentle manner as he walked over to the person occupying the hospital bed. Shinichi stood next to the agent, not really sure what he should be feeling. Shūichi then opened them when he said: "Or rather, I never would've thought you were an Omega, Gin."


To be continued...


1)) Sensei can be used to address both Doctors and Teachers.

2)) Neechan basically means Big Sister in Japanese.

3)) Keibu basically means Inspector, mostly used with police.