Rawk's right, in the game itself more than the Master Sword could harm him. Here, the "only the Master Sword" thing was for Bee's phase of the battle, when Ganondorf actively maintained shielding, and the Master Sword outright bypassed this shield.
If you'd have read Ajax's sheet, Jon, you'd know that if Ajax had interfered with Bee's phase he'd have decimated Ganondorf. The fact that his personality prevents it saved the entire battle. Ajax can overpower magical protections and immunities with brute force. Also, Ganon is Ganondorf's final phase, it's just another form of Ganondorf's, so there really isn't a difference between Ganon and Ganondorf. I've been looking at exactly what Zero's been doing and none of it has been outside of the limitations placed on him (in this case, mostly personality-based limits, which works every bit as well as physical limitations).
Now would you kindly drop this subject? You're the only one with a problem here, so that ought to say something at least.
EDIT: Anyway, I'll be bringing in a guy that won't show up until we get out of the digital universe. He's a canon character, but can be placed in a Multiverse RP without breaking any lore at all, nothing special done, nothing. He's gonna help the newcomers get familiarized with how things work in the Multiverse. He's also skilled enough to fit, as he has killed would-be gods before.
EDIT 2: And don't think it's just Jon that's the problem. Zero, I do want you to hold back on the attempts to outright kill. Chaos was understandable (and has a habit of coming back from the dead anyway). From now on killing as well as resurrecting player characters must be approved by me since it's appearing to become a problem. I do manage to at least do OOC checks daily and manage OOC stuff, it's mainly IC that I can't do a bunch of posting daily (which is why the IC is collaboratively GM'd), so you don't have to worry about waiting too much.
I realize this looks like me stacking limitations on, but it's mainly me correcting oversights with the original system.