In Chapter 1072, Vegapunk says this to Bonney in regards to why he can’t say why he turned Kuma in the past:
If I divulged the reason.. it would only serve to hurt you!! That’s why I can’t.. I promised Kuma that I would keep his secret from you no matter what!!
Later, Bonney says this when she gets in front of the giant paw created by Kuma’s powers and responding to Vegapunk’s obvious bluff:
I know my father’s ability all too well. His memories are here, aren’t they?
This is where my theory begins. Oda is about to bait the reader. We think that we are about to get Kuma’s memories and a flashback from Kuma to clear the air and to unravel the mystery of his character, and I agree, but it won’t be as straightforward as that.
Those memories aren’t Kuma’s memories. In the past, he took out Bonney’s memories so she wouldn’t have to bear the pain of what she did (presumably) that caused Kuma to be like this and his sad fate.
A hypothetical scenario would be that when she was younger, she might have done something recklessly which led to her and Kuma getting punished as he wanted to protect her. This makes sense as the Government already wants Bonney in some regard, given her interactions with Akainu, in some specific way as well.
The real tragedy is that Kuma just decided to keep all of his memories for the sake of his humanity because he didn’t want Bonney to bear the guilt of being the cause of Kuma’s pain and suffering.
The memories the reader is about to see in the upcoming chapters will be a Bonney flashback through her lost memories that Kuma took away.
It is a classic One Piece-style bait and switch coupled with a tragedy that was staring at us right in the face.
*Theory by meek_31