[story spoilers] Is there a plot hole about Kaliban and Rubycon ?

[Ragnaman]

So, at the start of chapter 5, Idaho asks what happened to Strain A, and Kaliban tells that some Kalibans killed Idahos, but I thought thats impossible because of Rubycon

Or I have not yet found something and that was a hint that there is more that they are hiding ? If so, then thats fine, I was just taken aback by this seemingly random text out of nowhere, and Idaho does not even have an option to ask about this fact, which seemed like a huge plot hole out of nowhere.

Then again...there have been plenty of hints that Kalibans are not OMNIs at all, so they dont have no Rubycon..., now im trying to spoiler myself,

In any case, what annoys me, is that Idaho does not immediately raise a question about what Kaliban just said. He does not question the Rubycon or Kaliban being an OMNI.

[Commisar Jon Fuklaw]

There are a few hints as to the truth of this matter, most provided by Kaliban, and the remainder pointed out in the final exchange of the game. Which is the absolute truth of the matter is disputable.

The largest hints or probable conclusions can be summarized thusly:

1.) Kaliban is quite capable of various forms of deceit and is seen to lie in regard to most major plot points. As an unreliable source of information, it is possible that Kaliban lied about RUBYCON and other expository points. RUBYCON was clearly not as immutable as it is made out to be, given the events leading up to the game, which I shall not detail because doing so would negate any reason to play the game unless you really like the combat system.

2.) The Emperor had contingencies in place to override RUBYCON in the event that his contingency plan was threatened by Idaho, as an example of Xanatos Speed Chess (look it up).

[Ragnaman]

Ok, I believe the Kaliban could lie, but why does the protagonist simply ignore this critical bit ? First thing that came in my mind was to ask about this contradiction, and it felt like a plot hole.

[Xaneorath]

Well, I think its the Option 2 which Commisar JF mentioned. I do believe Kaliban had Rubycon enabled, BUT with a few exceptions programmed into it. One of them would be "kill, if not killing would harm the backup plan". Thats what happened to the Alpha Strain. When they realized their situation, Kaliban calculated that the contingency plan was endangered by that development and decided its time to "scrap" the Alpha Strain and start anew. I believe the dialogue before chapter 5 makes it clear, as the Kaliban were pretty much discussing doing the same thing all over again, but only decided not to because their own time was running out.
Also there is the second override "kill, if the Emperor is endangered", which is made blatantly clear multiple times during chapter 5. It answered your question between the lines, and I believe thats why Kaliban repeated it that often. He WAS implicitly answering the question you had (because probably Idaho would have the same), and I believe he quite understood what Kaliban wanted to tell him with that.

So .. no. Kaliban did not lie, I believe. He couldn't just generaly kill humans (including Idaho), because there was never a situation that actualy endangered the contingency plan. If a ship fails there was still more room for new ships/clones as long as Gehennas Location wasn't compromised. He just omitted a tiny exception to the rule.

[Ragnaman]

I understand that, my question is about why the protagonist suddenly does not question this on the spot, but seemingly forgets and accepts that "oh well Kaliban can akshully just kill me if I decide to sneeze at Emperor in an abstract way".

This paradigm shift should change how Idaho perceives Kaliban COMPLETELY, but its ignored.

[Xaneorath]

Eh ... no, I don't think so.

First of all: No, Kaliban could not kill Idaho on the spot, as long as he does not see danger to the contingency plan or the emperors life (I doubt sneezing suffices. ;). That being said: He might even not be able to shoot Idaho at all, because he knows that the plan will fail guaranteed if the Beta Strain fails. So there is no logical reason for the "kill, if the contingency plan is endangered"-failsafe that may override his Rubycon.
And thats exactly what I think Kaliban communicated between the lines while mentioning the Oberon-rule, he was communicating that he cannot just shoot Idaho on a whim (anymore).

As for Idaho ... I think its reasonable he played along, as Kaliban got it quite right: They needed each other at that point.
I think another thing Kaliban said ~between the lines~ was that Oberon is the only one who can deactivate Idahos Limiter, giving him a strong reason to proceed with the plan. They still both had the same goal.
I personaly don't think there are any questions unanswered in that regard, so whatever would Idaho question?