I just bought it as I wanted to play it as nostalgia. I play and all that happens is that I see a small portion of the screen in the top left. I cannot do anything. I see my mouse move and I see parts of the menu, but nothing works and I can't read it.

Have you checked the specific subforum yet?
https://www.gog.com/forum/star_trek_armada_ii

Someone else might have had the same problem and got it sorted with the help of others. If not make a new thread of your own.

Sorry I haven't. Is my first time posting on GOG. Thank you for showing me.