Ok, cause at some point it's like we have to break up with after getting back together. It seems counter intuitive and really messed up to abandon him like that.
the question that determines your ending is the last question of his route where you're at the train and your choices are "we'll work something out" or "its over". if you chose "we'll work something out" which is his bad ending you can try doing the "it's over" option which is the best in my opinion.