I think a lot of people here are confused.
The actual story:
Lightning struck the tower, the tower was set on fire, it started raining, the fire went out. (I seem to recall the detail that the fire or the rain lasted three days - can't remember which. Not important, though.)
The only living things that died in the fire were Raikou, Entei and Suicune. Ho-Oh revived them and, in the process, gave them powers that *represented* the event - Raikou was given the power of the lightning that struck the tower, Entei was given the power of the fire that burned it and Suicune was given the power of the rain that doused it. That's what >>37172779
was getting at - obviously the Beasts didn't cause the fire, but they do embody those aspects of it in canon. (Fun fact: that's also the reason the Pokédex orders them Raikou -> Entei -> Suicune - it's the order of those elements in their story.)
This also implies that they couldn't have been the Eeveelutions, because the point is that they DIDN'T already represent lightning, fire and rain - people often cite that similarity as proof of the theory, but it's actually pretty strongly implied that it's the opposite of what happened. (That said, there's technically nothing proving that they weren't regular Eevee given Ecruteak's affinity for them... but I'm not personally sold on that. Personally, I really don't think they were ever meant to be any *specific* existing Pokémon before they were reborn, any more than, say, Keldeo was supposed to be a Ponyta that got transformed by the Swords of Justice - obviously Keldeo didn't have Justified or Sacred Sword before it learned from them, so obviously it was somehow different before they took it in, but that doesn't mean it was anything we know about or ever will.)