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I don't know the exact quote but i believe Okita tells Kodai that all the department heads were killed in the bunker and i did read somewhere that those now in command were chosen last minute from the crew.
As for the warp meeting, everyone from the main bridge staff was there except Ota. Poor guy, must be feeling left out. XD And it would make more sense for him to be there than Nambu since the navigation section has a bigger role to play in the warp and he is assisting Shima on the procedure. But i'll venture a guess that he was left steering the ship (or watching Analizer). XD
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