So the routes were the protagonist could point out who placed the bombs had been unlocked: he mentioned the terrorists and revealed that Dio is the bad guy. He activated bombs, and only by reloading various point in the story I could gather the instances where he had revealed the deactivation codes. This eventually led to the proper ending, I don't remember why I had to switch to another timeline.
In the other timeline I entered the third chamber, for the third time with Luna on my side, and then chose Ally. In the chamber I found out that Luna is a robot. Afterwards Phi, Quark and I (the survivors apart from Luna) could escape, and we did but Sigma changed his mind in the doorway and went to talk to Luna. As things turned out, in this storyline Alice had died from Radical-6, Luna had battled Clover and pretended to die, as per her master's instructions, and Dio had killed the rest of the people. Then I got an emotional discussion about that Sigma meant a lot to Luna, and it meant a lot that I trusted her. Aww.
In the storyline where all the bombs were deactivated, it was eventually revealed that the old woman who we found dead in some timelines but did not find in others was saved by us, Sigma and Phi, transferring our consciousnesses to the past to just before Dio killed her. We save her, and got a tiny key. We then all played enough prisoner's dilemma games for everyone to have the required points to leave (except Dio, who was left behind) where Tenmyouji explained that we were not in a desert looking at the Lunar Eclipse, we are on the moon looking at Earth made red by nuclear war, in the year 2074. We entered the facility again (apparently you could just go down an additional floor in what I felt undermined the whole story) and using the key we unlocked a pod where someone was in suspended animation.
K in the robot suit then revealed a whole lot of the plot and it turns out that in the timelines where the old woman was not killed she took the role of K, in storylines where she did not the guy in the pod took that role, hence revealing why they were different people in this storyline and in K's ending. The old woman was Akane, the person that arranged the last nonary game and she revealed that this one was set up by Zero so that Sigma and Phi had enough training to go back in time and stop the initial spread of Radical-6. Zero, as things turn out is, the player character Sigma aged 67. Or rather he will be once he has naturally aged to the current age; at the start of the game his 22-year-old self's consciousness and his 67-year-old's consciousness switched bodies, and the game has conveniently not shown his face up until now: he is an old man with a bionic eye. Then they laid out a plan of what he should do to hopefully avert the apocalypse.
---
Some highlights from my previous speculation:
"I suspect [the old woman Akane] was [Tenmyouji]'s wife. And that Quark is his grandchild."
Wrong on both counts. While she was his long lost love, they were not married, and if anything Quark should be considered his child, since he more or less adopted him.
"I don't think the old man Tenmyoty[sic] is the bad guy though. "
Correct.
"I suspect Phi is going through the game again and again since some comment she made alludes to this and we found a book on Schrödinger's cat."
I give myself a half point but that was a question the teacher only put on the test so that everyone could feel like they understood something.
"I also think the player character has gone through it again and again since exploding moon base dreams could be the bomb that was found in the Alice route."
The bomb did indeed cause the explosion on the moon base, and another friendly teacher half point.
"The game here presented the question of who I thought had killed Luna. I said Clover. "
I was correct in as much that Luna pretended to be dead from the attack from Clover. I don't know how the game would have reacted if I had picked something differently.
"[my explanation for the string of murders] falls down on the rather boring 'Quark did it in a fit of Radical-6 induced madness', but that does not explain how he was able to kill Dios and K. I think the authorial intent is that I am supposed to feel incredibly lost. Clover had apparently written 016 on her thigh before dying; I have no idea what that means. "
I was wrong about this. Also: Clover actually wrote "dio", on her thigh, but it was transferred to her other thigh mirrored and they never checked the first thigh.
"
Who do I think Zero is? At this point, I don't know.
[---]
Finally: am I Zero? That is one of those far out twists that I imagine the author giddy, jumping up and down with excitement on the prospect of pulling it off, but I don't see it happening, unless it's some sort of self inflicted amnesia where the events are set up to happen in advance, but that sounds ridiculously improbable.
"
This reasoning was the last in a series of each candidate and I mostly threw it in for sake of completeness. With that said: that was QUITE accurate.
"The sights Sigma has seen has led me to believe that this is set on the Moon... though one with artificially increased gravitational pull, but the broadcast made me think that either this is set on Mars or in a Nevada copy of the Mars base."
It was set on the moon as I speculated, though I deserve no points for this since I went with another theory.
I have not mentioned this before but: they had an explanation for the gravitational pull thing. EVERYONE in the facility had been infected with Radical-6, which makes your brain experience time differently and therefore thinking the gravitational forces were normal. I never wrote it but I wondered if I would eventually discover what Quark did to get the infection that latter spread to Alice, and get the opportunity to prevent him from catching it in the first place.
"New theory: we're in a scenario everyone tries to avoid: one in which Radical-6 spread and caused a worldwide pandemic causing a total of 6 billion deaths. These Nonary games are repeated in some way to make sure the disease never spreads. How this all sticks together and how this information could be passed through time I don't know. In that case our mysterious Zero might actually be a good guy, trying to save 6 billion people, by putting people in the sort of circumstances that activates the time-travel-communication. Though the "Scientific theory" has not yet been brought up by the plot so new players would be lost if that is the case."
This theory turned out to be mostly correct, it wasn't conversation with the past that was the key aspect. High 5, fellas!
"Tenmyouji also seemed to suddenly show a greater deal of care since he voted Ally "because Clover was on he other team". Is he also playing this visual novel?"
Yes and no. He is also an esper, I don't know if he did any consciousness transfers but his reasoning for caring for Clover is because he recognizes her from his past.
"I also think it is obvious that Tenmyouji is Quark's grandpa."
Wrong. My certainty does not do me any favors.
"Given that he knew about the Mars mission and seemed to think all is lost once Quark got Radical-6 I suspect he's a key figure in this arrangement, no matter if he's Q or not. Since his grandchild is named Quark I therefore suspect him of having brought the bombs in."
He was a key figure in this arrangement; if Akane is to go by all but Quark was, but I meant more in terms of knowing what goes on behind the scenes or being an assistant to Zero. This was wrong. He also did not bring any bombs in.
"HOLY MACARONI THE PROTAGONIST IS A ROBOT! Most likely. Since I've never seen Phi bleed and she can perform super human feats in leaping into the air and, most importantly, she retains memories from different routes, it would sense that she is also a robot. That both Sigma and Phi are Greek letters also indicate a connection between them. Hu-bot model φ and model σ or what have you. "
Sigma was not a robot, he was an old man. Neither was Phi.
"I'm currently leaning towards Phi planting those bombs."
Incorrect.
"Random idea: in some routes we find the device that could deactivate the bombs. I'm thinking the bombs only appear when Zero has access to that device, and analyzing what safe it came from might be fruitful, and whom went to that chamber."
Incorrect. Zero did not place the bombs, and he who did it always had access to the bombs.
"What I think happened is that the room I spoke with Clover in was a sort of pressure chamber to keep Radical-6 from entering the facility, but in her eagerness to get to Alice she did not do the proper precautions and everyone got infected."
Incorrect.
"I was earlier going to say that since Phi was able to vote differently depending on your vote in the Prisoner's Dilemma then maybe that was indicative that Alice also had the ability to transfer consciousness between nodes, but since Tenmyouji did the same it sounds like it would be a stretch to have that many people changing the past."
It was not a stretch if you ask the game's writers.
"I have had the thought that this is in the future, the people that are robots did not require suspended animation to get here and Tenmyouji is old so he actually took the slow route, which would make him the architect behind it all. If Phi and Sigma are robots that would still mean that three more people are robots, but they still bleed, so I think that's crazy talk."
It was indeed crazy talk.
"Though now that I think about it: in this ending Sigma committed suicide by slitting his throat and the graphics showed a splash of red on screen. Does that mean his arm is robotic but his torso is not? That could imply that a lethal injection from the bracelet would not affect him."
A lethal infection would kill him, even though his arm was cybernetic.
"What I think happened is that [Tenmyouji] also triggered the hologram (which might have had a different message for him) and from this figured out who Zero was."
He did. He saw Sigma speaking claiming to be Zero.
"So K, Sigma, Tenmyouji, Quark or Dio? Or a third party? I'm lost. "
I want to claim victory on the grounds that I even mentioned the protagonist here.
"For the overall plot, my current idea is this: ahead of SOIS' raid on the terrorist HQ SOIS figured that if the Radical-6 virus was as devastating as their intel suggested, they would need to have a way to get a cure quickly. Researching medicine takes time (decades, if that journal is anything to go by), so what they did was to play a Nonary game in 2028 with the intention of using the time travel powers, once a cure had been found, to play a Nonary game anew and transfer the necessary information back to 2028. That is the Nonary game I'm playing. I wonder if many participants had been in suspended animation since then."
SOIS were not the chief architect behind this nonary game. And only three people had been in suspended animation.
"If K and Sigma look exactly alike and K worked in genetic research I'm thinking that one or the other is a clone."
Correct
"Maybe I actually am playing Sigma of 2028 experiencing the clone of the far off future where Radical-6 had had their cure found, via the homomorphic/telepathic field?"
I am 2028-Sigma in 2078-Sigma, no clones involved.
"I also wonder if there's a connection between Alice' father and K since they were both researchers."
Nothing of the sort found.
"Since Dio could be revealed as a killer at the beginning of the game I do not think he is Zero. He is intended as a red herring, someone everyone suspects because of disagreeable actions but not the greater scope villain."
I was dead wrong. He was the only character I can safely call a villain.
"I also had a random thought: flashbacks are in general shown as drawings whereas regular conversation and in-game cinematics are done via 3d-models. I prefer the drawings, but I wonder if this is indicative of something, like those are the only parts of the story that are not in some way artificial. I speculate since my YouTube feed keeps recommending a video called "Virtue's Last Reward - Hiding in plain sight" which makes me try to look for something so obvious that you don't even reflect on it."
That was not a clue.
"At this point I wonder if Zero even is among them, the more important aspect being who performs what actions and why."
Zero was among them, but the more important aspect as a player was not that.
"Since Dio was an infiltrator, I'm thinking the intention was to transfer the cure back to 2028 via the Nonary game, something the terrorists did not wish so they therefore sent Dio to stop them from changing the past. I now wonder if I am playing the real Sigma from 2028 who directs the protagonist in the future of what to do, since the protagonist often wonders why the heck he did a course of action that he did."
The first part correct, the last part incorrect.
"Earlier we noted that three (3) people had used pods recently, meaning only 3 people should have gotten here via suspended animation. The fact that there are two people with the same appearance, K and Sigma, makes me think they are from the future year, K having grown up in the facility leads credence to this. Tenmyouji aka Junpei aged naturally to that age. Dio is a fourth generation clone so he's from the future year. Clover was put in suspended animation to connect with Snake in 2028. Quark hooked up with Tenmyouji when the latter was old so he is from the future year. Phi is aware of different timelines so she's probably an agent, could be from either time. Alice was probably put in suspended animation. Luna is the only question mark. The fact that the future year is a post apocalypse probably mean that the level of technology has remained relatively static and looking at their backstory reveals little."
Got this mostly right.