Um, I could be wrong, but by the sound of it, I get the impression that you think once you have beat the game- even once- that's it, it's over. You can load the last file you saved on, leave the crater, beat the WEAPONS and THEN come back down to defeat Sephiroth again.

If you mean that, after you beat Sephiroth, can you load the game back up into a Sephiroth and Jenova free world in order to explore or kick the WEAPONS' collective asses, then... no.

If none of what I am saying makes sense, please make sure to swiftly ignore my babbling. Thank you for your time.