It is my personal hypothesis that PKMN Trainer Red died on top of Mt. Silver before encountering the player character in Gold and Silver.
First, when you speak to his mother in Pallet Town, she's reveals that she hasn't heard form her boy in ages. She off-handedly dismisses this absence of communication as "No news is good news, right?" (hardly a healthy parental attitude...but, then again, children are sent off on dangerous death marches at the age of 10, so...) When you investigate his room, you discover that his PC is closed, and caked in a film of dust - this corroborates his mother's story. Red has truly been away for months, possibly years.
Second, look at the place where you confront him - atop a precarious ledge, in the surging hail. This obviously isn't the sort of place where a healthy, living teenage boy would choose to camp out, much less await a worthy opponent, if that is his aim. No, he's there because he's somehow tied to that spot. I believe this is the spot where he met his end.
Lastly, observe his behavior. This is evident both in the original games and the remakes. He may have been a silent protagonist in his game, but one has to admit that his eerie greeting of "........, .........." is more than a little off-putting. What happens when you finally defeat him? The player momentarily blacks out, and Red disappears into the ether. It is my belief that, once he meets a worthy opponent capable of defeating him in battle, his soul is momentarily put to rest. Of course, this reasoning does not explain how he respawns after defeating the Elite Four. Perhaps he is responding to the player's battle with Lance, an opponent whom Red struggled with in the past?
So, Red finally makes it to Johto after becoming Champion. He climbs Mt. Silver in search of adventure, but the mountain proves to be too great an adversary. Whether he died of hypothermia brought on by the extreme cold, or he lost his footing on the mountain's peak, I don't believe he ever made it off the mountain alive. Indeed, the Johto champion isn't battling Red himself, but the restless spirits of Red and his Pokemon.
You can say: ¨but you battle him in PWT, in the champions tournament, your argument is invalid¨.
But... Is that so?
Think about this: When you see him, he says ¨...¨, when you battle his Charizard, he says ¨...!¨ and his final quote when you defeat him is ¨...!!¨. Even Blue has real quotes, as far as i remember. And the ¨...¨ are strange if we consider that the announcer says that Red is ¨A living legend between the champions¨. If that is true, then he would have to say something better than ¨...¨, right?
But the icing of the cake, my fellow trainers, is when you win the tournament, and then go to the inferior left corner of the PWT room. In that place, all the trainers you have defeated in the last tournament are seated. But, when you battle Red, his chair is ALWAYS empty. You can speak whit all the trainers, but not with Red, because he never appears there.
So, what are your theories? What happened to him?, --- Very Boring
He's alive. The people who made the game made him talk like that because they wanted the player to fill in the blanks in his quotes.
As for how he disappears after you battle him, he obviously figured out how Giovanni pulled it off (it's the same animation), and is doing what Giovanni did to disappear. --- http://i458.photobucket.com/albums/qq303/CharizardFire6/Char-Brawl.gif The official Charizard of the Pokemon Black 2 and White 2 boards.
Red was born with a deadly genetic mutation that prevents him from speaking. He also got bitten by a galvantula(don't ask) and gained its powers letting him jump off Mt.Silver after losing only to climb up again after ethan beats the e4. --- The Offical Groudon Oof the POkemon Black and White 2 Boards.