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The Main couple and the ML's older brother went to school together as kids. They were 2-ish years apart from each other. Japanese schools are 6 years of elementary, 3 years of middle school, then 3 years of high school. So this means while big brother was a 2nd year in highschool, ML was a 3rd year in middle school and MC was a 1st year in middle school. Just at the beginning years of puberty.
The ML teased the MC because he kinda liked him, but this lead to ML friends seriously bullying him. This and his withdrawn personality lead to MC's middle school years being hell. Even after the ML pulled back from the teasing, his friends, now full on horny teenagers, began to be not just cruel, but predatory towards him as an Omega. This disturbed the ML because he genuinely like the MC as a person. But at this point he didn't know how to protect him. So it seems he tried to build MC's confidence and defend him from the shadows, but the ML (and all his shitty friends) graduated before anything romantic could form. But these small acts of kindness left an imprint on the MC. ML graduation day is also when the MC had his first heat which caused a panic. After he was given pills to stop his heat, he hid behind the gym and the ML gave him his coat to cover his crying face. They then parted ways for many years. MC is traumatized by the bullying, but also infatuated with the guy who started it all.
Fast forward to present day. MC is working at a company that designs and makes clothes in the underwear department. After college and some time as an adult Omega, MC is no longer as shy and weak as he was in highschool. At least, towards everyone but the ML whom he still is traumatized by. ML, who was in human resources, sees that he has a second chance at protecting/romancing the MC, but still doesn't have a clue how to go about doing that. So he forces his way into becoming his work partner to be closer to him at least. This leads to drunken sex and misunderstandings. Still, feelings develop between them more deeply as they work together.
Eventually, ML starts pulling away so he doesn't accidently mark the MC as his mate. He's pretty sure the MC likes his older, kinder, brother after all. MC and him hash out their feelings and (assumedly as it was a fade to black deal) have heat/rut induced sex in the office leaving the MC marked. But the security cameras caught everything and they had to break up their work partnership.
They move in together at the very end.
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It makes more sense now thank you so much I really appreciate you taking your time and explaining to me I was totally confused I was thinking that the seme wanted to be with the uke but just couldn't because it was prohibited or something in that way. I don't know it was a mess in my head thank you greatly appreciate it(づ ̄ ³ ̄)づ
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Just one clarification, the ML did not mark the MC (he bit the MC's hand but that's it) because he said he wanted to be together with him without worrying about being mates.
Which is a nice touch, I feel like i have only read one other Omegaverse where a couple got together and did not mark each other as soon as they found out they had mutual love. They date each other for a long time before finally mutually deciding the day they would become bonded.
I'm not sure what I read I am totally confused I didn't understand anything I don't know I don't understand why maybe I'll try re-reading it but I don't even know what happened in the manga I'm so confused(⊙…⊙ ) ┗( T﹏T )┛ ヽ(`Д´)ノ