He wasn't sure why it had taken him so long to realise it. In the end, he came to the conclusion that it was due to a mixture of repression and distraction.
Even as Shinichi, his life had been turbulent. But since becoming Conan the sheer amount of cases he got entangled into had increased considerably.
Homicides, kidnappings, robberies - he ran into a different case almost daily. And with time the cases got more and more absurd. How many bombs did he have to defuse in the last year? He had been shot at more often than he could remember. He had been thrown out of a zeppelin. Hell, he had jumped from one half of a ferris wheel to the other and survived! A derailing train, being buried alive by an avalanche, jumping from a skyscraper with a car, more than once one might add, landing a passenger plane on a pier - sometimes even he himself couldn't believe the situations he had been in.
His life felt almost surreal. How was he supposed to focus on himself when he was constantly busy saving others?
Apart from that, his quest to destroy the organisation demanded most of his attention. With new allies appearing it took more effort to keep his identity a secret. Together they followed new leads, encountered new members of the organisation and had a few confrontations that almost ended deadly.
Weeks turned into months and suddenly a whole year had passed. He was frustrated that he was still stuck in this body. Ever since Haibara had come into his life, he had believed that she could create an antidote in no time. Apparently it was more difficult than either of them had expected.
As Conan he had always been a bit smaller than his classmates. Sometimes he got mocked for his size by other children, but the Detective Boys, especially Genta, always came to his defence. He was intimidating enough for others to leave him alone. He could brush the comments off without a problem, since they weren't too far off from the truth. He was abnormally small, at least for his real age. The whole concept of looking up at others felt unnatural to him, it was something he had to get used to in the beginning. But he spent a lot of time with teenagers and adults, people whose height didn't change, so he could continue pretending that everything was fine.
With the Detective Boys it had been a gradual change. As time passed, he had to put his head further and further back to see Mitsuhiko and Genta properly. But it was normal, right? He was just a bit smaller, he would catch up to them eventually. Even when he barely reached Ayumi's shoulder he still ignored it.
Only after the annual examination by the school nurse, when he saw his measurements black on white,irrefutable proof, was he finally forced to face reality. He hasn't grown at all since becoming Conan.
It triggered a new fear in him. Since that fateful night he had had one goal - to track down the people responsible for it and get his body back. Sometimes, after a new failed experiment or an unsuccessful confrontation with the organisation, he thought about the possibility of a different life. One, in which Haibara would be unable to create an antidote. He would have to let go of his identity as Shinichi Kudo, of Ran and his friends, but otherwise he could still have a relatively normal life. Growing up a second time with the Detective Boys by his side would have been bearable. He could have learned to accept it as punishment for being careless. But not growing at all? It was akin to a nightmare.
After the examination he had dragged Haibara aside. He noticed that he could look her in the eyes - filled with so much pity and guilt - without straining his neck.
"You knew." He felt betrayed and didn't even try to hide it.
"I thought you did too."
It was a reasonable assumption. He was detective, after all, he was supposed to notice the smallest discrepancies.
"Is there nothing you can do?" He asked, even though he already knew the answer. She would have shared it with him if she had something, anything, because she still felt responsible for his situation.
Still, the simple shake of her head hit him harder than any bullet before. The weight of this new knowledge crushed his last hope for some kind of happy future.
His mind was spinning, wondering how he could have missed it the whole time and trying to come up with a solution. He barely noticed that he hadn't run into a new case on his way home.
He entered the agency, his home for the last year. It highlights once again how much time had passed. Ran was already waiting for him, sitting on the couch, wringing her hands and a worried expression on her face.
"Welcome back." She forced a smile on her lips. "How was your day?"
"Like any other day." He said and took his shoes and backpack off.
"Oh, that's … that's good. Do you have a moment?"
Conan nodded and dragged himself to the other couch, sitting down opposite of her. He was careful to avoid her gaze.
"Your school called me today." It didn't take a genius to deduce what they had told her. "I blame myself, you know? I should have noticed myself. We were too inattentive, because you always seem so grown up, like you can take care of yourself without help. But we … I took you in like my little brother. I took on responsibility for you and I failed. I should have paid more attention to your health." Her voice began to shake towards the end. Conan glanced at her and saw the tears threatening to escape her eyes.
She stood up and began pacing in the room. "Maybe it's the stress from all the cases Dad drags you to. Or you're not getting enough nutritious food. Maybe it's the coffee, or -"
"It's not your fault." Conan said firmly. He had caused her enough grief already, she shouldn't feel responsible for something she had nothing to do with. "I think it runs in my family, something genetic." It was as the only explanation he could think of.
"Why haven't you said anything before?" Ran got on her knees in front of him and grabbed his hands. Now he could see the tears she couldn't hold back anymore. "We have to get you checked out by a doctor. There might be a remedy, some kind of drug they can prescribe you. Growth hormones or something. "
If the situation wasn't as dire, he might have found her suggestions funny. He couldn't tell her that he had been tirelessly looking for a remedy for the last year.
Ran didn't let herself be fazed by his silence. "I've already made an appointment tomorrow with a specialist. He might be able to help you."
She squeezed his too small hand and smiled encouragingly at him. Conan nodded, numb. He didn't have the strength to take away her hope. "Thank you."
Her smile faltered. "Don't be. It's the least I could do now. I should have done something earlier." She wiped away the tears. "I'll leave you to your homework now and for dinner I'll prepare your favourite dish, alright?"
"Sure."
He held it together until the door to the room he shared with Kogoro fell close behind him.
Since he had realised the whole scope of his situation, he could only think of one way to get out of it. He had hoped that he would have more time, at least a few weeks to make it easier for everyone, but the impending doctor's visit forced him to act faster.
He couldn't be seen by a doctor. For one there were the changes the APTX4869 had caused in his body, traces of which were still detectable in his body according to Haibara. But the external condition of his body would be even more difficult to explain.
He stared down at his arms and torso that were covered by a long sleeved shirt. He knew what lay underneath it. His skin was covered in countless scars, mementos from all the life-threatening situations he had been in. The most prominent was the gunshot wound on his stomach. Grazing shots, explosions, broken bones, falling from different heights, getting beat up, a few burns - all these things have left their marks on him.
During a thorough examination he wouldn't be able to hide them and any competent doctor would react immediately. Police and child protection services would be called. The Moris would be questioned and blamed for his disastrous condition. They would start digging into his past, trying to locate his neglectful parents and they might realise that Conan didn't really exist.
Immediately after his first run-in with Gin and Vodka, Agasa had asked a friend to forge a few documents for Conan. They had been pressed for time and it was only supposed to be temporary cover. He doubted that they would withstand a proper investigation by the police.
Alternatively he could tell Ran everything about his true identity and involuntary rejuvenation. But with the threat of the organisation still looming over him he would put her in unnecessary danger. And where would it end? Even if he told Ran, it wouldn't stop the curious questions from all the others who would sooner rather than later also realise that something was wrong with him. Was he supposed to tell everyone?
No, there was only way to keep everyone safe. For the rest of the day he put his best poker face on and indulged Ran in her need to pamper him without a single complaint. He ate two portions of her cooking and made sure to mention several times how delicious it was. Before going to sleep, he hugged her and thanked her for everything.
For hours he lay awake, starring at the ceiling and listening to Kogoro's snoring. Ran checked up on him three times. Every time he pretended to be deep asleep. Finally it got quiet in her room, the bugging device he had planted in her room earlier didn't detect any noises. He waited a few minutes to make sure that she was really asleep. He quickly got up and crept through the room. As quietly as possible he packed only the essentials. He had thought about preparing everything earlier, but he had feared that Ran might notice something. The whole time he watched Kogoro closely. He had his wrist wratch ready, prepared to tranquillize him at the first sign of him waking him.
When he was done, he placed a letter on the kitchen table where Ran would find it first thing in the morning. He waited a few seconds in front of Ran's room, the desire to see her for the last time fighting against his rationality that insisted that it was too dangerous, that it could wake her up.
In the end he left the agency without looking back.