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In general omegaverse, knotting isn't needed, it only increase the rate. And idk if the heat is needed but Jea in had been injected with a drug that put him in a heat state.
And about the baby disliking his pheromones, i do agree that seems to point he isn't the father, but it's not a proof at all. It could be random or the baby acting this way because of Jae in.
Anyway, I said he technically could be the father, not that it was likely to be the case. But he probably called the baby "his" because that's the way he thinks he can get closer to Jae in.
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Damn don't add more delusions to Choi the doctor tracked the weeks he became pregnant and it aligned at the date they did it when he was in heat plus Taeyoon is the more dominant one, you'd assume it's his seed that won XDD plus Choi knows he isn't when he asked the doc what happens if the alpha is separated to the pregnant omega, he's just coping
Well technically, it could be his ? Or was it confirmed it's Taeyoon ? I did assume it was Taeyoon's because he was the one to help stabilize Jae in during pregnancy but maybe it didnt have to he the father.