I know the little boy in Men in Black 3 was J and it's implied that K raised him. I was fine with that implication until I asked myself... "why didn't J's mother just raise him?"
So, my question is, why didn't J's mother just raise him?
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I don't think it is actually implied that K raised J. Rather than that, it seems to imply that he silently looked out for him behind the scenes his whole life, until he recommended him as an MiB recruit when he was old enough.
If I remember correctly, the movie implied that the events from the 60s in MiB 3 always happened (rather than being some kind of new timeline). So J's first actual meeting with K would be when he applies for MiB and becomes his partner in MiB 1. There was no notion of them knowing each other beforehand.
So I think the implication there was really that K just became somewhat of a silent guardian to J out of responsibility for his father's death but without ever directly interacting with him. More like keeping an eye on him out of the shadows.