What follows discusses the ending of Spider-Man: Brand New Day in full.
Zendaya and Tom Holland worked the press tour for Brand New Day as a married couple, and the trailers leaned hard on the state of Peter and MJ. The film does put the relationship at its centre. It just refuses to tie it off.
The spell is still holding
MJ has no memory of Peter, and the reason is the bargain he made at the close of No Way Home, when Doctor Strange erased him from everybody's recollection. Four years on, nothing has undone it. MJ has finished at MIT and shares a flat in New York with Ned Leeds, played by Jacob Batalon. Both of them remember Spider-Man pulling them out of danger during their school years. Neither has any idea who Peter Parker is.
There is a boyfriend, briefly
Peter turns up uninvited at Ned and MJ's housewarming and sees her kissing someone. The film gives the man a single scene and never names him, which is the film telling you exactly how much he counts.
The letter sets everything moving
Jean Grey, played by Sadie Sink, is a telepath, and she finds the letter Peter wrote at the end of No Way Home and never handed over, the one explaining who he was and what the two of them had been. She uses it as leverage and threatens to walk into MJ's mind.
Peter reaches her first in costume and talks her into leaving the flat. Somewhere safe, she asks what they were to each other, then takes off his mask. He kisses her. When Jean does get into MJ's memories, she confirms there is nothing of Peter in them.
The rejection is stated outright
MJ finds the letter herself later on and is angry, mostly that he sat on it for years and might never have said anything. Peter tells her he was trying to protect her, that he loves her, that she is everything to him. Her answer is that she understands why the woman in the letter felt what she felt, and that she is not that woman. She tells him she does not love him, and that she does not even know him.
And then the door opens again
She trusts him enough to let him take her home, and then invites him up to meet Ned, still in the mask. Peter and Ned end up building with Lego, the old dynamic returns without anyone remarking on it, and MJ sketches the pair of them. In the sketch, Peter is not wearing a mask.
Two smaller beats push the same way. Earlier in the film MJ mentions that her boyfriend accuses her of withholding things. Later, when Jean freezes part of the city with MJ inside it, a tear runs down MJ's face while nobody else caught in the hold registers anything at all. Readings of that moment split between worry for Peter and memory coming back.
The last shot
Peter wakes in hospital after the final fight and finds MJ's sketch of him and Ned beside the bed, so she has been in to see him. The film closes on MJ alone on the rooftop where the three of them sat at the end of No Way Home, holding the broken black dahlia necklace Peter gave her in Far From Home and wearing it, as she had been at the housewarming. She is smiling. Nothing is spelled out. Everything is placed.