It was a 3D PS2 game where a blond guy in red (the protagonist) and a kind of iron (or stone) golem had an objective (I don’t remember what it was). I also have some flashbacks that the protagonist had one stone arm and used it as a sword.
I THINK the bosses were a snake, a giant bird (and I don’t remember the other one, but I think it was a frog), and at the end of the game the three bosses merged and turned into a giant purple slime.
Each boss was in a different area. I remember that the bird boss was at the top of a prison, there were caves, a castle, a tower that, going to the top, led to the final boss, which was the purple monster, and sewers that led to a snake (I think).
from your description it seems to be: Fullmetal Alchemist and the Broken Angel