I like Cloud stealing the Fusion Swords from the guy who forged the Buster Sword. It is an old tradition (at least in several fictional references I can think of) of master smiths that when you make a sword, you make two, one inferior which is sold as normal, and a perfected version which is kept as a showpiece to show off your skills or dedicated as a holy sword in a temple somewhere. Hell, Klepto Strife might have taken it from a shrine in Wutai where it had been placed in memory of the Midgar-Wutai war for all we know.
I admit, I used to have a silly theory about the Masamune (at least I thought it was silly, it closely echoes some things said here). Namely, that it and the Ultima Weapon were both forged during the war between the Cetra and Jenova, but none of them could actually use the Masamune, and The Planet, when it was making Ultimate WEAPON, somehow incorporated the Ultima Weapon into its form. Oddly I always figured it was one of the critter's claws. Anyway, the Cetra did somehow beat Jenova, so the WEAPONS all went to sleep in the Crater until needed again. But, what to do with the Masamune? It was essentially useless after all. So, when they sealed Jenova up, they basically nailed her to the rocks with it in hopes of keeping her "dead" as it were. When Shinra found Jenova and ran the Jenova project, they found this awesome weapon too, but again, no one could use it for shit. Blah blah, Jenova Project, Sephiroth is born, grows up, becomes the first SOLDIER, and of course they say "Hey, this dude we so cleverly created, who will of course never go crazy and try to kill us all, is like hella-strong. And we made him out of cells from that freaky thing we for some asinine reason thought was an Ancient, which is where we got this sword. Maybe HE can use it." And the rest of course was history. Like I said, silly and somewhat overly complex theory, but fuck it I was like 15 and over-thought things cause I wanted an explanation for this kinda thing damn it.
