When she finds Salieri at Mozart's side, she orders him out, against what Salieri states is Mozart's will. It is during this episode that Mozart dies and since nobody was there to plan anything about his death or funeral (his father was dead and his wife gone away) he was buried in a mass grave and that was the last of Mozart.
A slightly more cheerful relationship was the one that Mozart had with his father. At a very young age, Mozart was learning everything that he possibly could from his father (musically speaking). The two were very close as was illustrated at the beginning of the film. Mozart's father was pretty much always his protector and really remained true to him until his death. His father did not want him to leave his side to go to another job and another place. When Mozart was dismissed from his original position, his father went back and pleaded to get him another chance, and he eventually did. When he told Mozart of the opportunity that had been reopened, his son did not listen or even appreciate what his father had done. Eventually Mozart's father came to live with his son and his daughter-in-law, but that was a true mismatch. It seemed at though the both Mozart's father and wife wanted to advise him on what to do, but their ideas always conflicted. In the end, Mozart's wife wound up basically asking Mozart's father to get out of their house. To me, it appeared that Mozart's father was always doing what he could to give his soon a good life, but his son never bothered to listen or head any of his advice. Shortly after Mozart's father moved out of his son's house, he passed away. To the viewer, this episode really helped decay Mozart, his life, and his career.
More hateful than any other relationship in this movie was the one that Salieri had with Mozart. Even though Salieri always acted in a civilized manner around Mozart, the viewer could see the developing tension and hatred that was being conjured up in Salieri's soul.