Desdemona awakens, and Othello asks her if she has prayed that night (line 26). Although Othello intends to kill Desdemona, he does not want to kill her soul. That is, he does not want her soul to go to hell. If she has prayed and confessed her sin to God, then she can still enter heaven. But if she dies without confessing her sin, her soul will end up in hell. Othello, despite his anger and madness, does not wish that upon Desdemona.
When Desdemona realizes that Othello plans to kill her, she asks heaven to have mercy on her (lines 35-36). Othello appears to agree with her because he responds with “amen” (36). The word amen is traditionally used in Christianity at the end of a prayer. The word suggests approval or agreement. But Desdemona and Othello are expressing two entirely different views with the word mercy. Desdemona is expressing her desire for God in Heaven to restore Othello to rational thinking so that he will not physically kill her. But Othello is suggesting that he hopes God will have mercy on her soul and allow it to enter Heaven.
When Desdemona continues to tell Othello that she is innocent, Othello becomes angry and completely irrational. He has become so completely convinced by Iago, by Iago’s his false evidence, that he believes that Desdemona is not only unfaithful, but a liar as well. And, so, he no longer offers Desdemona the opportunity to pray and confess. Rather, he smothers her with a pillow (line 92). This is the climax of the play. Desdemona is not quite dead at this point, but she is dying.