Check around the six-minute mark on this video (everyone else stay far away -- final boss battle spoilers).
Hmm. It looks like I merely need to take the damage, dodge (although it looked like the guy was getting smacked by the projectiles), and hammer the boss... although I imagine harder difficulties will require more cycles of this and thus be much more difficult.
(Opens 3DS cautiously...)
(Dies again... but after a bit more time)
It still looks like the guy is getting hammered by projectiles there.