Happened to see this while browsing for Tales of Destiny.
Unfortunately, I haven't played the game in quite a while so I don't remember city names, etc. I do remember taking the time to kill Leon to get this ending though. Instead of doing it with a save glitch, I just walked to one of the other towns and bought a stack of 20 Energy Bullets to kill him.
You can only hold about 15. E. Bullets and they have a dmg range of about 200-250 each. which is rougly 3-4K of his health and Leon has 9999 HP. Which would still require you to level up some in order to do decent amounts of damage outside of E. Bullet spam to take him out. The save corruption glitch lets you come back with a power leveled party that can do good dmg to leon and make short work of him. Thanks for the tip though :v)