Was Battle Command Centre aware they were dealing with an extraterrestrial civilization?

Question

Early in the book, protagonist Wang Miao is introduced to Battle Command Centre and given to understand that there is some kind of war or struggle going on, although he's unclear who or what they are fighting. However, according to ex-cop Shi Qiang:

Those in charge are terrified! I know General Chang very well. He's the sort who's afraid of nothing, not even the sky falling, but I can tell that he's worried about something much worse right now. They're all scared out of their wits, and they have no confidence that we'll win.

At this point all that is apparent to the reader (and Shi Qiang) is that there is some sort of conspiracy aiming to disrupt and discredit scientific research, which could have an entirely mundane explanation. Globally, the response seems disproportionate to this, to the point that normal geopolitics has been completely sidelined:

NATO officers are now stationed in the war room of the PLA General Staff Department, and a bunch of PLA officers are working out of the Pentagon.

Clearly, some kind of existential threat to the whole world is anticipated. But did they know that it involved extraterrestrials, or did they think it was merely a human political conspiracy?

Answer 1

It's not explicitly confirmed in the novel, but as you say, the level of response is out of proportion to anything but an existential threat to the human race. Later in the book we learn that the ETO, or at least members of the ETO, are confirmed as being behind at some of the elements of the conspiracy. The basis of their organisation (e.g. aliens) aren't exactly secret, albeit the world's governments have historically viewed them as largely a band of kooks.

In order to grow fast, the organization operated semi-openly, but the governments of the world never paid much attention to the ETO. The ETO knew that they would be protected by the governments’ conservatism and lack of imagination. In those organs wielding the powers of the state, no one took the ETO’s proclamations seriously, thinking that they were like other extremists who spewed nonsense. And because of its members’ social status, governments always treated it carefully. By the time it was recognized as a threat, the rebels were already everywhere. It was only when the ETO began to develop an armed force that some national security organs began to notice it and realized how unusual it was. Consequently, it was only within the last two years that they had begun to attack the ETO effectively.

With low-level agents inside the ETO, world governments would have learned about the Trisolarans and their plans for invasion. This isn't a secret internally.