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Even though I agree you're forgetting that Omega's feromones affect alphas and make them go into heat/rut as well. It seems like the seme is not really that badly affected by them, but if we consider the possibility of him being "drugged" and seduced by the feromones it's understandable enough that he was unable to control himself. At least in every other omegaverse manga if an alpha smells and omega's heat they'll immediately lose their reasoning and try to bite or mate with the omega. Though some end up biting their own hand or something but others became maniacs. But the level of control differs quite often between different on the manga artists.
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True, altough I've noticed that the usual drama omegaverse has is pretty toned down in this story, plus this guy can reason enough to literally stop, put on a condom and continue. I do think he could have stopped, because in fact he did, he just chose to go on afterwards. I guess at least he's being careful...? I'm not attacking the alpha behaviour tbh, he's is probably the tamest I've ever read of lol but I don't blame the omega either, out of the two he's definitely the one who has literally no grip on what he's doing. I guess it's understable if he feels like the one who had more control should have stopped the thing
and then he's gonna blame the alpha for taking advantage of him 'again' even tho he's the one who came to him first... what's else new??
sometimes i feel bad for good alphas like him XD