[Chango]

Originally Posted by SoLiDUS

I'm not exactly sure how it would happen in the real world, but a baby can
just be linked to those two specific beings once loaded in the program. It's
something I thought about as well... I wonder if they'll answer it for us ? :-\

Edit:

A long shot, but consider the idea that sperm is forced out of the human
male (the same way I assume they handle urine and fecal matter) and it
is redirected to the female linked to him so she is "artificially inseminated":
how they remove the child and all that shit isn't really hard to understand
afterwards.

in the first matrix Morpheus said humans are no longer born, they are grown(or something similar to that)