To beat the secret boss (aka the glitch) you need to equip your characters with nonelemental weapons. I used the level 5 chainsaw blade with Matt, the level 5 chainsaw gun for Lance, and the starting staff(too lazy to check what its called) for Nat. First and foremost, DO NOT use ANY attacks that have an element. They wil all heal him. If you can, have Matt use his Cleaver Limit Break, which at max level will take him down to about half hp on epic difficulty. Make sure Nat has starshower, because his little minions have next to no hp, and are easily slaughtered by it. Once you know this, he's basically a joke. use coffee when need be, and you have the fight in the bag.
I loved this game when I first played it, and i'm just now getting back to it thanks to the colonial marine badge challenges. Also, WOOHOO! NEW ENDING!