After her conversation with Miles, the governess stays outside the church and reflects upon their conversation. She thinks that he knows he “got something out of” her, or that he knew she was afraid of having to bring up why he had been expelled from school, and she expects him now to use that fear of hers against her as a way to gain freedom for himself. She says she wishes she could bring up the issue with the boy’s uncle, but the prospect of doing so was too much for her to handle.
The governess’s suspicion that Miles has been keeping a secret from her, and conspiring with Flora, has now escalated to the fear that Miles is taking advantage of her. She sees his beautiful and innocent exterior as a kind of weapon he’s now using in his own favor. Her unwillingness to report anything to the uncle shows her continued shielding of the children and desire to show her ability to handle this on her own.
Because she is so shook up by her interaction with Miles, the governess returns to Bly, leaving Mrs. Grose, Flora, and Miles behind at the church. Upon entering the home, the governess notices a stranger seated at her writing table. To her horror, the woman in the black dress is Miss Jessel. The governess calls out to her, calling her a “miserable woman”. Miss Jessel disappears.
That Miss Jessel is seated in the governess’s chair here is significant. It enforces the idea that the governess sees in the ghosts a kind of challenge to her authority as the primary person responsible for the children.