Are you familiar with the concept of "Fridge Brilliance"? TV Tropes defines it as:

You watch a movie and something about it just seems off, you don't like it. One night, as you get up for a midnight snack, you open the refrigerator door and the light dawns on you, "This is the real purpose behind this plot!"
Because you had that epiphany, what once was a hated moment has become one of your favorites.

... and this game is choke full of them. Well, maybe you didn't hate them, but there are certainly some moments or some things a character say that, at the time, did not make much sense, or you perceived them as odd, but in hindsight get a whole new meaning. Which have been your favorite moments of such fridge brilliance? Obviously, again, SPOILERS! I won't bother putting hiding anything behind a spoiler tag because you've all been warned. My two favorite ones are:

• Sigma and K: K is Kyle Kline, Sigma's clone. But when the group finds him, nobody recognizes his face. Sigma's mind is blown... and it blows even harder when he looks at his reflection in a well and realizes he's an old man with a cyborg eye. With this knowledge (and everything that is revealed in the True Ending), a lot of unusual things make a lot more sense:

1. The 3DS lower screen looking like a scanner, due to Sigma's eye.
2. The fact that the only time we see his face is in the intro, but never during the game. Even when he accuses Dio of being the one who planted the bombs the player only sees his arm stretching, à la Phoenix Wright.
3. Someone in the Crew Quarters (I think it was either Alice or Phi, can't remember) mentions that it had been "a long time" for Sigma to still be working on getting his medical degree. Given the fact that he's only 22, at first, this comment seems a bit out of place, since you don't usually finish your degree until you're 23, 24 years old (or even older, in the case of Medicine). But then you realize that Phi and Alice see Sigma as an old man and their comment gets a whole new meaning.

• Why Luna always chooses Ally. She's a GAULEM, so she has to go by the Three Rules of Robotics. She will never choose Betray, since she could be indirectly harming a human by doing so.

I just got why everyone got so creeped out by all of Sigma's sexual innuendos.

My favorite moment aside from the one you already said, when you look at your reflection, is probably the reveal of the whole plot and understanding why and when your conscious did all the jumping back and forth from different bodies. I just need more time to properly articulate it, the end needs some time to sink in.

I also loved how this game is kinda just about the how the whole Akane being alive and dead at the same time thing works, it's Schrödinger's cat the game.

@Linkster7 said:

I just got why everyone got so creeped out by all of Sigma's sexual innuendos.

This.

It also gave me a completely new perspective on Clover. That part where she says she'd go on a date with Sigma seemed kind of cute when it happened, but after that reveal I was like "Wait a minute..."

But I think the big one is the fact that Sigma doesn't have a voice actor. It really bugged me when I first started the game and it didn't make any sense considering everyone else had a voice actor, but in retrospect it makes perfect sense, as it would be pretty obvious something was up if you heard him speak, especially after you actually meet the Zero hologram. Although it does make me question why Sigma didn't notice his voice was different.

@Zeik said:

It also gave me a completely new perspective on Clover. That part where she says she'd go on a date with Sigma seemed kind of cute when it happened, but after that reveal I was like "Wait a minute..."

HA. So much to question about that girl.

@Zeik said:

Although it does make me question why Sigma didn't notice his voice was different.

I wasn't too into the twist of his voice not being heard just so that the player couldn't hear it, but the fact that Sigma himself couldn't tell that his voice was different, that he didn't notice that his body might have some changes and additional wrinkles and the fact that he never saw his reflection in a wall or touched his face even once—immediately noticing that he would have a damn robot eye—kinda ruined it for me.

@FluxWaveZ: Well he had cybernetic arms so I can give the wrinkles a pass and they did explain that the lower gravity meant he wouldn't notice the strain of old age as much. I can even give the not touching the face (not like I touch my face often) or seeing reflection a pass since that's possible, even if perhaps unlikely. But the voice thing is something I can't think of any explanation for.

To be honest, it probably would have been better to give him a voice actor and then come up with an explanation as to why it didn't sound like old Sigma.

Ok,I just finished finished it, all those old man comments in the game nice hints, whenever they siad that i thought, "what the hell im only 22", although kinda impossible to realise until the end i guess. The whole voice and reflection stuff is a stretch i guess but, i suppose since its a sci-fi game i'll let it slide.

But on your luna point, On the luna end she states that she let all those people die when she could have saved them because she was scared, so its reasonable to asume that she could have chosen betray but never did. also she calls you doctor which is a nice hint.

But god dammit that ending, I'm referring to the true ending (another time END), I'm guessing that the dude who you are in it, mister ?, might be the protag of the next zero escape game or something, and might be 'you', as in the player (you) time jumping into game character perse that would be nuts.

Also i'm bummed out they never reveal anything about phi, who is she man.

I think this might be my GOTY.

Isn't there a point where Quark calls him an old man as well? Obviously the player is meant to take that in the manner that Quark is a little kid and to him everyone is old, but it was the first hint I remember.

@Zeik said:

It also gave me a completely new perspective on Clover. That part where she says she'd go on a date with Sigma seemed kind of cute when it happened, but after that reveal I was like "Wait a minute..."

Oh MAAAAAN I never even thought of that! But she doesn't actually do annnnnnything you want, either.

But I think the big one is the fact that Sigma doesn't have a voice actor. It really bugged me when I first started the game and it didn't make any sense considering everyone else had a voice actor, but in retrospect it makes perfect sense, as it would be pretty obvious something was up if you heard him speak, especially after you actually meet the Zero hologram. Although it does make me question why Sigma didn't notice his voice was different.

Yeah, but while I knew that there was a reason why Sigma wasn't voiced from the very start (because in these games, nothing like that is coincidental), I didn't know exactly why, so the twist was still a decent surprise. I very much expected him to be a robot (the "memory bank" memo section and photographic memory was explained easily with that) but nope, just a cyber arm.

I really liked VRL. I wasn't expecting the time travel aspect to it. And I love time travel. That made me go back and play my unopened 999. I think its intresting that they call it the "True Ending" considering that in order for that ending to be "true" the other endings have to have happened. And that means they are also True.

The whole reveal with the reflection would've been a lot cooler if it wasn't the exact same twist from an earlier game.

@DonChipotle said:

The whole reveal with the reflection would've been a lot cooler if it wasn't the exact same twist from an earlier game.

Ah, I never played Uchikoshi's previous games, so it was a complete surprise to me :P

@Rodin said:

But god dammit that ending, I'm referring to the true ending (another time END), I'm guessing that the dude who you are in it, mister ?, might be the protag of the next zero escape game or something, and might be 'you', as in the player (you) time jumping into game character perse that would be nuts.

That's Kyle Klim, aka K aka future Sigma's clone. It looks like he has somehow "inherited" Sigma's alternate reality-jumping abilities... or something "else".

Edit: OK, I should elaborate. The body is Kyle's, the consciousness in it... I have no fucking clue. It could be a new character, it could be a character that's already been introduced in the series. We want know for sure until the next game is released. But if what I think it right, Kyle must have the ability to send his consciousness across time, just like Sigma, in order for the ?-(wo)man to inhabit his body in the first place. That seems to be old Sigma's plan all along.

@Rodin said:

Also i'm bummed out they never reveal anything about phi, who is she man.

One of the golden files mentions that there are hints to who she is throughout the game, but I never figured out what they were. But it also implied that we'll probably find out more in the next game.