Manato sat there, watching everything unfold. Everything to the point where they arrived at the familiar tree and the dragon awaits. Everything happened so fast that he didn't expect things to end that way. It was like he watched a movie, and then everything went to a dark ending.
Also, seeing the Goddess of Death lie down weakly on the tree made him feel the urge to protect her. Although Manato did not know her personally and only learned and experienced her actions via the eyes of the baby dragon which has grown to be a majestic black dragon, he can still feel that the Goddess of Death doesn't deserve all of the hatred she accrued.