Spoilers ahead for the February 24 episode of The Good Doctor on ABC, called "Autopsy."
The Good Doctor wasn't easy on Shaun throughout "Autopsy," as he struggled with the fallout of his breakup with Carly, tried to figure out how to tell Lea he loves her and wants to be her boyfriend, and pushed boundaries to try and autopsy the body of a woman whose death frustrated him. By the end of the hour, he mustered his courage and dropped the big L on Lea, but it didn't go as he wanted.
Lea looked desperately sad even as she told him that she loved him too, but she said that they couldn't be together because she was too selfish and too much of a mess for him to handle. Shaun understandably interpreted her response as her saying she couldn't be his girlfriend because of his autism, and Lea was too overcome to answer him when he asked her that very heavy question.
Freddie Highmore, who plays Shaun and also directed "Autopsy," explained the "horrible truth" of the final scene between Shaun and Lea to EW:
That last moment, that’s so lovely [because] there isn’t anything to say. It’s so heartbreaking because it’s this horrible truth and what I think that Paige [Spara] did such a wonderful job at in playing that moment is that we feel for Lea just as much as we feel for Shaun. I think Lea realizes just how there’s almost a sense of self-hatred there like, ‘I know that I shouldn’t be feeling this, and this is a horrible thing to admit, but if I’m completely honest with myself maybe it is partly because of that.’ That seems to make that moment so powerful because it’s this genuine, horrible thing that she has to admit.
While Lea does love Shaun and told him so, she couldn't lie to him (or herself) and say that she thought they'd be good as a couple. In other circumstances, her silence after he asked if she wouldn't be with him because of his autism might have turned sympathies firmly away from Lea, but her clear honesty and devastation at having to say these difficult things to him proved that it wasn't a black and white situation. I know I felt for them both.
According to Freddie Highmore, Lea's reaction to Shaun's confession doesn't make her a horrible person. He raised the point that "We’re not horrible people for not falling in love with everyone we come across," and the relationship with Shaun is complicated to the point that there are "certain things about Shaun she just would not be able to put behind her." She loves him, but doesn't see a romantic future for them as of "Autopsy."
That's not to say the will-they-won't-they dynamic of The Good Doctor is doomed forever due to the events of "Autopsy." Freddie Highmore went on to say there's still hope for the future between Shaun and Lea:
I also think there’s a real sense of confusion that Lea is left with at the end of the episode. I don’t think it’s as clear cut as, ‘This is it. It’s all said and done.’ I think she doesn’t respond because she doesn’t know what to say. There is a horrible truth behind Shaun’s question that she’s left with and she doesn’t know how to respond to it, because I don’t think it’s as simple as yes and no. By not responding, it does leave the door open a little bit. I’d like to think so anyway. Certainly from Shaun’s perspective, I don’t think he takes away from episode 16 the idea that this in any way is over or that there’s no hope left.
The conversation ended, but not really with any sense of closure or that the subject would never be visited again. If anything, the events of "Autopsy" proved yet again that Shaun doesn't give up on getting answers when he cares about something. I'm not saying that I see him banging on Lea's window and shouting like he did to the man who was refusing him autopsy rights in this episode, but he may hold onto hope until Lea can definitively shut him down.
See what happens next for Shaun and Lea when The Good Doctor returns to ABC with a new episode on Monday, March 2 at 10 p.m. ET following the tell-all episode of The Bachelor. There are still questions of what's next for Claire, who has had a difficult season and is now dealing with the taboo nature of her platonic friendship with Dr. Melendez.