The captain? How could he do that? he surely was sedated by that time, and i dont think the first thing he would think of is to kill everyone... He could had used an axe, but it wouldnt make sense, it would be just stupid if he just kills everyone and end up trapped there...
I wonder, if i could read Junpei's description again maybe we could know what weapon killed him. Oh and the silhouette of the person that killed him wasnt fat, it was a tall and skinny person, you could see it from the water, and i dont think they would randomly put any sillhouette, beacuse when Ace explained how he killed "snake" we could clearly see it was one of the persons that held the nonary game before.
Ive been really thinking about that ending... I dont get it at all, first of all, why a submarine? when they were inside a building? Maybe someone (the killer) came from the submarine?
And there are still some stuff i dont get... the first time you see June, she know she is Zero?, if that is the case, she is a really good actor, but Seven still told the story like June died 9 years ago, so the June that was there now, how the hell was she there now?!, even after, from little Akane's point of view they were all saved, then she could become big and do the game, is like, there is a big hole in the time. Because there should be at least one "dimension" where Akane is actually dead...