Reverend Ernest Trelaw wonders if she'll stay, but Saul doesn't think she will. Outside the church, Emily Hutchings and Ace walk around it anti-clockwise, talking about various events and the Doctor's treatment of Ace. Emily asks why he's so horrible to her. Ace explains they were in the TARDIS lab. She had a new batch of Nitro-9 and the Doctor was working on a cube, and when she asked him about it he got angry and she left. She wonders if the TARDIS will still be there when she goes back and wonders if she cares. They sit down and wonder if other buildings are inhabited like Saul inhabits the church, joking that offices would be dull and pubs would be drunk. The Doctor appears and says in an even tone "I'm sorry. Forgive me." Ace seems to shake her head and leaves with him, telling Emily she'll be back, but Emily wonders if she will.
While it is not explicitly clear, it seems like the Doctor uses hypnosis to make Ace forgive him.
The story would appear to be set just prior to PROSE: Love and War, as it is mentioned that the Doctor is constructing a cube in the laboratory and has shouted at Ace for interrupting him. This cube whispers to him, (Prelude Love and War) and is presumably the same cube given to Ace when she leaves, that allows her to re-enter the TARDIS. (PROSE: Deceit)