Ehm, it is in fact written in my Boss guide already
"Important to know for all bosses is that each of them comes in three different versions: Mega, Giga and Tera. The Tera boss is the hardest and will only appear if you manage over 98% shot-down in an area first. The Giga boss will appear if you get at least 95% shot-downs and you'll get the weakest of them, Mega, if you get any shot-down rate below that. The version of the boss will be displayed in the "console" window just before the boss, in case you're curious."