Q74: Tenmyouji mentions knowing who Zero Sr. is in his ending. Did he see the hologram of Sigma?
If so, why did he not expose him then and there? And if not, who did he think Zero was?
Yes. When Tenmyouji and Quark return to the Director’s Office to get the picture, he sees Doctor Klim’s hologram. So he realized Zero = Doctor Klim = Sigma.
Maybe he didn’t tell the others because he could have potentially assumed that the others were in on it as well.
I assume he told Clover the truth after they escaped, since she escaped with Tenmyouji.
And the reason why he said “I know Zero very well” is because he realized that Sigma, who was present, was Zero, but he also remembered that he had met Sigma 45 years prior at the test site when he was still young.
That is why he had stated that he knows Zero very well. And the reason why he wanted to punish Zero is because he wanted to leave Zero/Sigma behind and trap him.