999/Nonary games spoilers
So I think I figured out an answer to who the killer is in the yellow submarine ending
It's Hongou in the past
How does he escape from the original boat? The submarine!
What have we seem with Akane? She physically manifests across timelines!
Ace kills the Cap in this branch but there's a 10th person who kills Junpei - people are like "Oh it's Alice" but it's not! She's outside the facility. Who else could it be than Hongou from the past, running away in anger?
999/Nonary games spoilers
The implication of this is real cool though because it means he kills his future self!!!