Most evidence is pointing toward Ace being Zero. There's a lot of reasons why:
- In the ending where you find Lotus dead on the bottom deck, you notice that her bracelet is gone. The game specifically makes a big deal out of this, asking "who would benefit the most?" Ace could escape the ship with just his bracelet and hers, assuming he's Zero and thus has a zero bracelet. This is after you've been given the option of unlocking door 1 on the top deck, where you find the "captain" who has a zero bracelet. Ace could have had time to retrieve it and then killed the other players before letting himself out with Lotus's bracelet.
- When the 9 Man dies, he specifically keeps saying that he was lied to, that he lied to him, etc. 9 Man seems to know a bit about the game even before it starts, as if someone had told him - and only him - information about what was going on. Ace specifically has to help the 9 Man in the beginning after he seizes Clover. This suggests to me that Ace spoke with him before everyone else got out of their cells, and then told him he would help him escape immediately. Ace, of course, did this with the sole intention of showing the other players the consequences of not following the rules.
- Further, 9 Man becomes redundant in terms of escape after a while, because in most instances, the digital root for 9 would require three people anyway. Adding another 9 doesn't change that. It really only works if you've got two people who are digital rooting to 9 to begin with, and even then he's still not entirely required if you assume the zero bracelet coming into play.
- Ace could have killed Snake. Again assuming Ace is actually Zero, he could have a zero bracelet on him at some point. The zero bracelet plus Ace's own and Snake's could have opened door three. Ace could then have used his altruism moment to escape to some other place on the ship to watch the rest of the game play out and/or leave it entirely, letting the traps and puzzles go on their own.
- Ace could potentially be the brother of the killed captain on the top floor. He says siblings sometimes don't look alike, and given the age of both men, it's possible they are related. This is a weaker piece of logic but I'm making it anyway.
- Ace seems to know a bit more about the ship and some of the puzzles than I'm comfortable with. Especially the stuff in the boiler/engine rooms.
- Ace is the one person who doesn't lose his temper, as if he knows he's safe at all times.
- Ace names himself after gambling terms. There is a casino on the ship. No other character does this.
- The letter's of Ace's name all appear in the words "cradle" and "pharmaceuticals."
- Zero wore a hoodied trenchcoat of sorts. This could potentially be Ace's, but this is also a weak piece of logic.
- Ace is the first to disagree with Clover's suggestion that Zero is one of the players, citing that "this is what Zero wants - to turn us against each other." Other players think Clover's suggestion isn't a bad one, so why does Ace disagree so quickly to it?
- It is possible that Ace is not dead in the endings where you find his body on the staircase amongst other players. He could have killed the others and then pretended to be dead, only to kill the remaining players as they returned.
- During one ending, he asks Lotus to go elsewhere with him. As you die after this happens, you cannot verify anything that happens afterward. It's possible he kills Lotus at this time.
Reasons why it couldn't be other people:
- Ruling out Snake, as he dies.* There was a lot of reason to suspect him previously, as it seemed like he wasn't truly blind and also knew a bit more about the game than seemed possible. Edit: I find it odd that Snake was the one to first notice the missing components of the REDs in the hospital room.
- Ruling out Santa because of his seemingly genuine worry about his sister. Suspected him previously because of his dickish attitude and weird aversion to the clover bookmark.
- Ruling out Clover because she's related to Snake, and thus undergoes a lot of trauma in the game as is. Of course she goes crazy in at least one ending so eh. Her suggestion about Zero being one of them could be a great use of misdirection, but I still think she's more of a psychological casualty than anything else.
- Ruling out Junpei because unless this is an Agatha Christie, Chuck Palahniuk, or Edgar Allen Poe story, the "unreliable narrator" route would be and annoying copout. Besides I've seen him die three times now, so I'm assuming there's little reason to suspect otherwise.
- Ruling out June because of how distraught she seems throughout the game.**
- Ruling out Seven because of his memory loss/memory recovery and because he is a cop. He seems the most likely victim overall given his relationship with everything that has gone on in the past, as if Zero wants revenge on him. He also seems, in all reality, the most innocent of everyone involved.
- Ruling out Lotus because despite her anger/aloof attitude (at least three instances where it appeared that she didn't care about anyone else's welfare), she ends up being very useful in several situations and has a lot of weird knowledge. She seems too genuinely interested in getting off the ship, and the kidnapping ordeal gives her less of an impetus to want to be on the ship. I do find it interesting that I never learned the name of her other kid.
- Ruling out 9 Man because I'm assuming he's dead and because, as I mentioned before, the utility of deriving a digital root of 9 makes him almost entirely redundant.
*: Clover says Snake has a fake left arm, but in describing his corpse - even after being told his - Junpei mentioned the ulna. This still bothers me, suggesting that he could be alive. This would also suggest that Zero is trying to screw with everyone's head by having fake dead bodies. This means that 9 Man could also still be alive somewhere. I also find it weird that the mannequin bodies behind door 7 have alternating left arms, which could be a nod to Snake. Clover also goes into the Locke's Socks paradox at that time, which I find a weird coincidence.
**: Santa at some point mentions that you shouldn't trust anyone, as "that person could be the one who stabs you in the back." I find that interesting given that one bad ending has you getting stabbed in the back after watching June die, who would be the person who would trust the most.
Unsolved questions:
- Who is the captain on the top deck?
- What is going on with the coffin? Who the hell is in it? Snake?
- Why are there two 9 doors, one of which shows up in the "Memories of the Escape" option? This suggests that there is reason to go through it before the other 9 door.
The presence of the gun in the coffin is very interesting, especially when paired with the fact that you discover both 9 doors after. The gun suggests that if there was any disagreement, one person could enact their will at any time. It also does away with the problem of having trouble arriving at a digital root of 9 if you had the wrong number of people.