I recall that this happened when the Hoenn region came out. It was all new, but nobody in my grade cared about the new Pokémon. Not even the starters! There was one, however Flygon. Nobody knew who Salamence was and nobody cared. It was all about Flygon!
When Ruby and Sapphire versions came out, nobody payed attention to the story mode. They all just played and went right ahead so they can get trapinch. Same with me. By the time I caught MY trapinch, (which I nicknamed Flygon because I was so sure I would evolve it) Everybody found out about Salamence. So I wanted a Bagon, too.
I remember putting trapinch in the PC and going right to Bagon. Everybody just loved Salamance. They all thought it was so much cooler and stronger than Flygon.
I spent all day evolving Bagon into Shelgon and into Salamance! I went back into my PC, and noticed that the Trapinch, which I never evolved, moved one box over on the PC. That was weird. I put it back in its place, and deposited Salamence right next to it. I saved and turned the game off.
The next day I noticed that Salamence was gone! I searched my whole PC, but it wasn't there. I thought it was in day care, but it wasn't. Nobody would've released it because Salamence was the bomb back then! I went back to my PC, and realized that Trapinch was now a Vibrava! Its name was still Flygon, though. The weird part was that it was only level 17. How could it have evolved? I didn't care at the moment, though. I was too busy looking for Salamence, but it was gone.
The next day I didn't play Ruby due to being discouraged about the Salamence incident. But when I got back on, something even stranger happened! The Vibrava was now a Flygon! How? It was still level 17! The Flygon's name was now "Manthel". I tried looking up the word, but got no meaning. Manthel? I thought this was some kind of practical joke, but none of my friends admitted to it.
I asked them if they released Salamence, but they gave me the same response. I asked everybody who knew about Pokémon and they said no. I decided to use "Manthel" in a battle. The game froze when I sent it out. I tried to turn the game off. The battery light went out, but the screen didn't!
My Gameboy froze like that for days. It eventually turned off, though.
When I turned it back on, I had a Trapinch in my PC. Its name was FLYGON. My Salamence was next to it. I decided to quickly separate the two without hesitation. Just as I did, my Salamence's name was now "MANTHEL".
Today I just found out who Manthel was, because when I got my USED ruby for the first time, I remember that the saved profile on it was called MANTHEL.
Perhaps this "Manthel" died, and was unhappy at the fact that I created a new profile as soon as I got the game. Or maybe MANTHEL was angry how Flygon was his favorite, but I didn't care for it.
It's a bit of a mystery.