In the Submarine ending,June had to be involved for sure,we just don't know who the other one was because we can't calculate that,but it would make sense if Ace or Santa or both were her accomplices.
First of all let's analyze the scene,when we enter the room we see 3 "persons" dead :
Clover,Santa and Ace.
1)So what could possibly happen ?We didn't hear any gunshots,so he couldn't have killed them with a gun,he had to kill them using another weapon,like an axe or a knife,how could he kill all 3 of them together,especially Ace ?(They were always together).
But on the other hand,Ace is a big guy,he could easily stab Santa,then Clover would probably pass out before he even touches her.
2)June,first of all why didn't the killer kill her in the previous room like everybody else ?Of course there are options to justify that,but there's 1 stupid thing,unless it's just a plot hole,why the hell did she not warn Junpei that the Killer was there ?Who was the killer ? And finally someone who was killed,doesn't go all lovey-dovey before they die.
And also pay attention,that when Junpei entered the submarine room for the 2nd time(after discovering Seven and Lotus's bodies),no one entered the room except for him,I'm sure these automatic doors make noise when they move,so it had to be someone in the room to kill him,which only leaves June.
One thing for sure - one person couldn't kill them all,he's not a ghost,he wouldn't stay unnoticed.
So it only leaves June+Someone
