Braums murdered that girl as a child, and so his parents faked his death because they were either afraid of him or too afraid to lose their son, (probably a bit of both). So they raised him in secret in a sort of pseudo-denial, so that they wouldn't have to lose their son for something he did when he was 8.
Stacey Menear (The Boy Writer) "explained" the Twist Ending Cosmopolitan-interview
So you had multiple endings in mind at one point.
I did. The doll was going to come alive. That was the initial thing, was the doll was
going to come to life and chase them around in a scary way. It just
never felt right to me. I played around with the doll breaking and a
spirit comes out. I think the reason I chose [the ending I did] was
going back to the '70s films that I loved so much. There's this one
called The Baby and another called Bad Ronald, and they're sort of
these strange horror movies more than straight-up scary [ones]. I
think horror movies now are mainstream. They never get really weird;
they'll get really violent, but they'll never get strange.
Half the fun of watching a horror movie like this is trying to guess the ending. What's the secret to artfully planting clues?
It's a balancing act. I did the draft, got to the ending, discovered the
ending just like the audience would, and then it was a matter of being
like, "OK, there's a guy in the wall — how could he live there?" I
don't know how much this plays to the audience, but when she's putting
his food in the freezer, that's supposed to be the place where [real
Brahms] gets his food. So, stuff like that. It's just reverse
engineering, essentially.
Were there any pushbacks on the script? Was there a thing you had to fight to keep in the movie?
They talked about getting rid of her losing a child; they didn't think
that was necessary at one point. And that was so important to me,
because it makes her staying there make sense. It's still not an easy
buy that she would stay there. But I think it's better if you
understand that she lost a child, she's going through something, and
she sees something in this doll, in this existence in this house that
can fill that void that she's feeling.
Why do you think Brahms's parents needed to kill themselves? Out of guilt?
Yeah. They wanted to find him a match. I don't totally know if this is
supposed to be his girlfriend or his mom — I think it's a messed up
in-between. But, yeah, I think they felt like they had fulfilled their
missions and they couldn't stay there any longer. This was never
planned. They hid this kid to keep him away from the police, and this
sort of happened over time, and then it got to this point that they're
horrified at what has happened and what they've become. At one point
in the script, Mr. Heelshire says, "It happened little by little, then
all at once."