I don't have the ROM or this patch. You hear that Square? I own no ROMs. So this is theory.

But I bet if you create a copy of your Chrono Trigger ROM, then run the program called Lunar IPS, click "apply patch", and then click on the copied ROM, it will patch it for you. It is irreversible and should not be used on an original.

I also imagine it's pretty cool, but since I have not played CT in so long I'm a bit confused as to what might be going on. It is still fun to run about and read new text nonetheless. And Magus flies when he runs, and really, who cares about anything but that?