I might be reading this wrong, but it doesn't seem like she killed him, she saw him get back with ayanami at p19, and choked him so hard she gave him brain damage apparently(his clothes aren't the same at p19, he has his admiral clothes and taihou is fully clothed), and maybe kidnapped him, which might explain the interrogatory at p12(they might simply suspect she gave him the brain damage).
Actual plot timeline seems to starts at p10/11, then it skips to p19/p20 , then back to p12, then it goes back to the start.