How do I get the good ending in DoNW?

my brother and i have had the game for about 4 years, and we finally arrived at the final 2 boss battles. i beat Richter, but now i battle Marta and Lloyd, using Emil. if i kill them, especially Marta, i get the bad ending (Emil stabs himself, turns into Ratatosk's core) my tanong is this: do i let them kill me? and is there something im not doing right?