BECAUSE IT'S REALLY COMPLICATED GUYS.
Alright, first off, everything covered thus far in fanfic- two years following that 'fateful' day, Conan still hasn't gotten a cure. He's a little (Kay, a lot) depressed about this, as Ran's going out of district for college and he's stuck in third grade...
Cue new classmates 'Koji Hisoka', 'Kiyoiri Matsuda', and 'Kira Nyugen'. Koji looks like Gin. Kiyoiri looks like him.
Kira's just blind and creepy.
Somehow, through a series of twisted events he was never aware of, someone cloned him (and screwed with the clone, resulting in a girl with a few traits of Turner Syndrome), and got both a distant relative and Gin shrunk. A year and a half ago.
Needless to say, things were weird enough BEFORE another poison was thrown into the mix- The 'DNA' toxin, thought to have been a complete failure but in all actuality the closest thing to immortality found. Koji was dosed shortly before fleeing the Organization with Kiyoiri. Kiyoiri, thinking the remaining to copies were candy of all things, gave one to Conan.
And then later snuck the last one herself. As it is, Conan's world is... Interesting. From finding out that a Jiang-Shi was the inspiration to Holmes and meeting it in person, to entering the underworld and coming back... All without dying!
He can't become Shinichi again. He'll be lucky to get any older than 18- after that the APTX stops fighting the DNA toxin, and immortality sets in. He's faked his death as Shinichi and grudgingly accepted his fate- though it doesn't stop him from lamenting the fact that Ran will forever be out of reach.
This depression resulted in an interesting 'friendship' between himself and Koji; it's a very volatile relationship, but they've saved each other's lives enough that they can't completely turn on the other. (It's possible after all, for either of them to drown, suffocate, or starve.) So they just... Beat the crap out of each other when it comes to the worst really (though Conan being Conan is much better about that.)
All in all, this Conan is more cynical than canon counterparts, and has strangely enough adopted a bit of Koji's 'crazy' traits. He fights more- legs being his main weapon, and in recent times is struggling more or less with a crush he's developed on Ai; and little does he know but Ai's been experimenting with what little information on the DNA Toxin she has...
Any questions? Send a PM! I probably made things more confusing as it is really.