Disclaimer and notes: I don't own Detective Conan. Setting is... throughout the series really, so there may be mild spoilers for some cases, but details are generally vague. This was spawned from the idea that there's more to Mouri than he lets on.
Playing the Fool
Mouri Kogorou was no fool.
Granted, he wasn't brilliant, and he certainly wasn't the great detective he was reputed to be, but he wasn't stupid. He knew when something strange was going on.
The first case that he had no memory of solving had seemed a little odd. When he had opened his eyes, he was sitting in a chair and Megure-keibu was congratulating him. He couldn't explain why he couldn't remember the events of minutes prior, but he tried not to give it much thought, passing it off as a unique oddity.
The second time, he chose to ignore it. It was just a coincidence that the missing memory was of solving the case like last time.
The third time it happened, he couldn't disregard it again. He wondered briefly if he had some strange illness that was causing him to forget things, or if he was working too hard and forgetting because of stress.
By the fourth time, he had decided to figure out what was happening. He was a detective, after all; he could certainly figure out what was happening to him.
He began to notice that he usually felt a small prick on his neck before the memory-less bouts occurred, and that he felt groggy afterwards. Combined with how others said it looked as though he were sleeping when he solved the cases, he concluded that someone must have been putting him to sleep with the pinpricks… but who?
Megure-keibu was out of the question. Ran as well, and the brat. But who else could it be, other than them? They were the only ones that were regularly there when he slept…
But then there was a time when he wasn't the one who was put to sleep. They had gone on a trip for Holmes lovers because of Conan, and that teenager from Osaka had shown up, looking for Ran's friend Kudo Shinichi. The Osaka detective had been the one to put on the sleeping show, and Kogorou watched. Megure and the police weren't there at all. Ran was by his side. Conan was nowhere to be seen.
And something was off about that Heiji kid once he'd slumped to the floor, his back resting heavily against a door. There was something not quite the same about the way he talked. His eyes were closed, and his head was leaning down, and he didn't move, save for raising his arm awkwardly and badly pointing at the perpetrator. When it was over, Conan reappeared from behind the Osaka brat.
Mouri Kogorou was no fool.
He started to pay more attention to Conan. The brat was always pointing things out, running around and asking questions. The kid was smart, and knew it. Whenever he started to let on exactly how smart he was and realized what he was doing, he would try to cover it up, suddenly turning back into a child. Conan's child-like behavior was just an act, he was convinced, but he still wasn't entirely sure that Conan was the one putting him to sleep. He didn't quite want to believe that the kid was the one solving all the cases.
But the kid was said to assist the sleeping Kogorou. The kid had been behind Heiji, and after that case where Heiji slept, he and the kid were oddly close. The kid had been there when Ran and Sonoko had gone to a meeting of an online magic-lovers club and Sonoko had pulled off the same sleeping act to solve a murder there. He was the only one who was always there. He was the only one who could be solving the cases.
There was still the matter of voices, as the child's voice certainly sounded nothing like Kogorou's or Sonoko's or Heiji's. But he was always hanging around that crazy scientist neighbor of Shinichi's, so perhaps he'd gotten some device to mimic voices from the old kook. Perhaps that was where he'd gotten whatever it was he used to put people to sleep, as well.
He wasn't sure how the child could be such a good detective at such a young age, but he knew it had something to do with Kudo Shinichi. He had seen Shinichi as a child often enough that he couldn't quickly forget what he looked like. Conan was a carbon copy of Shinichi—a carbon copy with glasses. Fake glasses, he'd discovered one evening when Conan had fallen asleep on the couch and he'd plucked the glasses off the kid's face to check them out. It was as if Shinichi had turned back into a child, with all the knowledge and experience he'd accumulated over the years.
And then, Shinichi had come back, and Conan was like a different person. The kid's abnormal behavior ceased when Shinichi vanished as suddenly as he had reappeared, and Kogorou was finally convinced. He didn't know how it had happened, or how it was even possible, but Conan was Shinichi, and he was trying to hide it.
Shortly after Shinichi's brief return, his suspicions were confirmed. He had woken up before the case was solved, and he sat with his eyes closed, listening to Conan-Shinichi explain the murderer's trick in Kogorou's voice.
He had heard Shinichi's solutions before. He didn't know why Shinichi was hiding or what he was hiding from, but couldn't possibly doubt the brat's identity.
The case after his early wake-up, it happened again. And in the case after that, and after that, and eventually the pinprick no longer put him to sleep at all.
But that didn't mean Sleeping Kogorou didn't make an appearance. When he felt the prick, he would play along, pretend to sleep, and listen to the kid solve the case in his voice. There was no reason for him to stop being Sleeping Kogorou, anyway. He rather enjoyed the fame, and he was actually becoming a better detective than he used to be by studying the brat's solutions—he had even managed to solve a case before the kid, locking the brat out of the room so that he wouldn't be interrupted. Besides, if he stopped playing along, who knew what the kid would try?
So he kept on as he had been, often suggesting that murders were suicides or accidents—not from really believing that they were, but from a hope that maybe this time would be different, maybe this one wouldn't be a murder. And when the kid wasn't acting like a kid, he would bop him on the head to provide a subtle reminder to stop being so damn obvious… and it certainly didn't hurt to get a little revenge for all those sleep-inducing pricks he'd been subjected to.
So he watched the kid examine the evidence, and he listened to the solutions delivered in his voice. And he studied. And he learned.
Mouri Kogorou was no fool.
He was no fool, but he was damned good at playing one.