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Who knows, perhaps ONI was directly a result of The Assembly AI and still under it's influence and guidance?
While the objectives of the single branches of ONI are quite known (section 2 has propaganda, section 3 research, development, special projects..), the true purposes of it's top head (or it's complessive purpose) remain unclear.
Even after Kilo-V there are still some shadowy facts about margaret (red flag, sanghelios colonization, the letter to halsey when she was deployed to infinity) that make me think we know nothing about her real purposes.
If the assembly knew about the flood they could have told somebody in ONI, but consider that both knew nearly nothing about the flood's nature.