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spoilers
there are actually 2 babies in the story. the 1st baby is a miscarriage because the uke was taking birth control on top of being recessive omega so he didn't think it was possible for him to get pregnant. the seme is a super dominant though which basically means his genes are super effective and managed to perform a miracle - sadly between the birth control and other medications he was taking it took a great toll on the baby and miscarried.
the second baby you find out about at the very end - the uke is pregnant with their second child, we just don't ever SEE the babies unfortunately...
LIARS WHERE IS THE BABY