"Chosen girl in a new and strange world" novel

I remember the cover was green. Most likely published in the late 1990s to early 2000s. I remember that it was one of those “chosen girl in a new and strange world” books. I remember it being fairly new. I remember the main issue was some evil something or other destroying planets or something. I remember them (3) standing in some space craft thing trying to make an important decision but the girl not knowing what to do (she must be like 14) and looking to the others for advice.