Some votes change depending on your vote - this is made a big deal out of with Phi and is part of how she and Sigma realise that they're both jumping around in time. They're affecting each other from multiple timelines, so they each incorrectly anticipate based on actions in other realities. Fine, that makes sense. But Alice (and, iirc, Tenmyouji) do the same thing at least once. In Alice's case, Sigma comments on how weird it was and talks about all the causality stuff. But why did her vote change? Not just her vote but the justification she uses for it seems completely out of keeping with the Alice who in every other timeline votes Ally in Round 1 (and gets betrayed for it). I was expecting this to lead to a reveal that other characters, not just Sigma and Phi, were also jumping around in time and that this is why they were all being jerks and betraying you at random, because they all had mixed-up information from other betrayals... but instead this was never dealt with. So what was going on? Tenmyouji and Clover at least had Esper powers so it wouldn't be hard to believe they were getting a little bit of timeline bleedover, but Alice isn't supposed to. So why did her vote change?
Okay, so the White doors were matched up with the bombs that Dio set up in Sigma's, Phi's, and Alice's endings. Well, it was revealed that the cast were infected with Radical-6 which slows down their brains to a degree of root-6. It makes sense that the doors would seem like it in the perspective of the people within it as Dr. Klim would set them up like that, but why would the bombs be like that too? Shouldn't they explode in their time limit real-time rather than Radical-6 time?
The only times the bombs are actually planted are in the routes where Akane was not murdered (the routes following the Cyan Chromatic Door), where Akane herself placed Dio in the AB Room and then put on the K suit. It is strongly implied that Akane slowed down the timers to compensate for the Radical-6. Note that the bombs do not have a clock face timer.
Just after the Security Room puzzle, Sigma experiences a moment where Phi appears sped-up to him. If they're all slowed-down by Radical-6 already, how can he be doubly-slowed? (Phi couldn't have temporarily recovered either as she was messing with the hourglasses at the time and would've noticed something was wrong.)
It's the same reason that Quark and Alice experience the same thing during their freakout(s) in the Infirmary. Odds are, Radical-6 symptoms can become much more severe in some persons than others.
How in the world did Sigma not notice himself getting a robotic eye, a deeper voice, and longer hair during the entire duration of the Nonary game? Even if he was feeling "out of it," those new characteristics are pretty hard to miss.
The voice is something he just got used to. The hair isn't much difference either (and probably isn't that long to show off the different hair color). The eye on the other hand is pretty unlikely to have not been noticed though. Zero Sr. probably should have invested in a replacement that completely fits in the socket rather than the one he wore.
What exactly is Luna doing when she's "dead" in Clover's ending? As a robot, she shouldn't be influenced by Radical-6 and would have no reason to kill herself. The only thought I can come up with is that Lagomorph took over, and have her act as a "human" by going along with the death. Though, she would be contributing a pile of white blood to the mix of everyone's red blood underneath her then...unless she didn't cut anything that bled...
Odds are that it's an order that Akane gave to her: "If the most/all of the players in the timeline you are in begin to succumb to Radical-6, you are to shut down immediately and not help them". To Akane, it doesn't matter if the players (including Sigma) all die, Sigma got the information he needed to gain the password in K's ending.
Which explains everything except the pool of red blood under her. I'm guessing she was altered, or she did something to make it look like, when she killed herself, that she was bleeding red.
More likely Luna was the last to "die", moved one of the bodies and shut down ontop of their bloodpools to make it look like hers.
When you choose "ally" against Dio with the Axelavir why doesn't Sigma think to use the Neostigmine if he discovered it was a cure for Tubocoraine in another route?
Phi mentions that it's not a guarantee that they will have access to all of the memories from alternate routes.
Not to mention that They didn't have the Neostigmine in that route, as the treatment center was never opened.
If Sigma gets the bomb code from his future self, where did his future self get the code? It's mentioned elsewhere that if his past experience is his only source for the bomb code, it creates a paradox because there is no original source for getting that information, e.g. from Dio.
They are separate worlds, an alternate timeline. If you use the analogy of the biker gang from the Another Time section, you can consider that opening a new path does not destroy what happened in the original event, but creates a different reality where all the bikers survive. Now you have two realities, one where most of them are dead, and another where they survive. Use of information from one reality to another requires specialized skill (ie Sigma's abilities), but is, according to the game's concepts on time, possible.
It's a little less complex than that. Someone mentioned that the password to that bomb decodes as name significant to Akane. So she probably changed the password on the bomb and the password was agreed upon before hand. Plus this is also evidence that Akane probably tampered with the bombs' timers so that they would work in Radical 6 time. All of this was pretty much confirmed via Word of God.
During Quark's route, Dio threatens to smash the Axelavir if Sigma tries to tell anyone he's blackmailing him... and then proceeds to leave Sigma and Clover's side for large amounts of time. Even worse, he goes into an AB Room (which is soundproofed) before Sigma and Clover do. So what exactly is stopping Sigma from pulling one or more of the others aside while Dio can't see/hear him, telling them what's going on, and then jumping Dio the moment he stepped out of the AB Room?
Simple. If he's immediately cornered, he still has an opprotunity to smash the Axelavir. And even if the others were let on, Dio still has his awareness. If he noticed somebody else acting unusually, he wouldn't hesitate in destroying it. And the others would most likely react desperately, especially Tenmyouji.
Why is it that, in the flashbacks in K's route, Dr. Klim isn't wearing the same robotic suit Kyle is supposed to wear in order not to let his muscles atrophy?
Maybe it's more important for K to do so because he's growing up on the moon, while Dr. Klim has been full-grown for a long time. We don't really know how moonbase environments work, so who knows, it could make a difference. Note that Akane doesn't wear a suit either. It's also possible that this was just a ruse to some degree, because Dr. Klim knew K would have to wear a full-body disguise during the Nonary Game.
It is indeed because K was born on the moon and would have otherwise had undeveloped bones. Akane & Dr. Klim had fully developed before they went to the lab.
Why did the Axelavir cure the Radical-6 infection in Quark and Alice, but they remain sick enough to experience time differently along with everyone else until the big reveal?
This is handwaved: apparently "some symptoms remain" after Axelavir is administered. Pretty convenient!
When one recovers from a major illness, their immune systems & body take time to recover. Same thing.
In Luna's route we learn that Zero Jr was ordered to move the AB Room. This seems simple enough, it's treated as a little strange but we're quite sure it was Zero Sr made the order. Only later on we find out Sigma is Zero. So did he make some off hand remark that Zero Jr mistook for an order? Or was it just because of the time travel he all the exact variables that had to occur for the plan to succeed?
It's the latter. In order to completely replicate the Nonary Game as Sigma had experienced it 45 years previous, Zero Jr was ordered to move the AB Room in the event of the murder of Akane. However, in the routes where the murder didn't happen, the AB Room never moved.
Sigma's true face is revealed when he bends down to look into the water in the B. Garden. Okay. So why didn't he notice during the puzzle in that room, where you're pretty much guaranteed to do the same as part of it? Or even just catch a glimpse of himself while waking over the bridges?
This is operating under the assumption that Sigma ever had a reason to look into the water, save for the Lion motif in the pond... during the day. The only time he looks at the water directly, it is dark in order to find the stars. It's reasonable there was no reason to go close enough that a reflection could be seen in the daytime anyway.
It's dark when the stars turn on, yeah, but they seemed to give off their own light. And for something that shocking, you'd think even a little would be enough for him to notice.
For a reflection to be cast on a transparent surface, such as glass or, in this case, water, a light source is required on the same side of the surface as the object being reflected. Since the light from the stars is coming from under the water, it is on the opposite side of the water's surface as the object in question, Sigma specifically, and therefore, no reflection is cast.
In K's route, who destroys Dio's bracelet? The characters hypothesize it was Dio's killer...who is later revealed to be K, who would have no reason to do so. Did Dio somehow break it as he was dying?
Word of God has it that K did indeed break it, in order to see who you would save: him or Phi.
VLR does a pretty good job of covering its tracks and keeping everything in order, but there was one small Plot Hole I noticed: Assuming she was telling the truth about it being a pre-recorded message, how did hologram!Akane know that the players would refer to Lagomorph as Zero Jr., when he introduced himself as Zero III? Granted, its implied she can also jump through time like Sigma and Phi, but I doubt she would do so for such a small detail.
Actually, it's the other way around. In at least six routes, including Phi's, K is the one who comes up with the Zero Sr/Zero Jr designations. And remember who was in K's armor in that route? Akane didn't make the recording to fit the name, she came up with the name to match the recording.
Why was the the entire Nonary Game important? Even Alice and Clover say it was important, and they don't get the satisfaction of revenge like Akane and Sigma do, but it's multiple timeline time travel, not "past gets overwritten" time travel. No one benefits from the whole thing.
While what you say is true, this isn't a plot hole. The game makes it quite clear that many people, including Clover, Alice and Tenmyouji think the entire thing was a very pointless and rather selfish affair, that gave no benefits to anyone from their timeline apart from Sigma and Phi. If the game never addressed this point, and acted like the entire plan was without any side-effects, then I'd agree that would be a problem, but as the game stood, it was put quite clearly in game as a negative trait of Akane's character and her plan rather then as an actual plot hole. So there's really no problem here in terms of plot.
Sigma not noticing that he's actually in an old man's body is consistent with the fact that most of the mirrors and water you discover in the various rooms are mentioned to be broken or dirty, thus he couldn't see his reflection. Though the above example of the pond in the garden could be justified by saying he probably didn't have reason to look in the pond directly/for long enough to notice, but... the puzzle in the crew quarters includes a sheet of aluminum foil that's said to be really reflective. So reflective that it's part of solving the puzzle. How did Sigma notice its super reflective properties without catching so much as a glimpse of his face?