Untreated mental illness
The novel starts right off the bat with this important theme; because the Great War involves warfare that is unequivocally traumatic, there is a dilemma in the medical field where some doctors see that clearly, the war is damaging people in ways they cannot explain. Other physicians refuse to admit that ailments can afflict the mind without any bodily source. The problem is that until this time, PTSD has not been discovered or discussed, so Prior lacks the vocabulary to explain that he cannot escape mental hell, even when nothing is wrong in the external world.
The person in chaos
Billy Prior is a person rattled by trauma and chaos, beyond imagination. His experience of war has no prior analogs, because WWI involves military technology which has been unseen before anywhere on the earth. He is a person lodged in chaos, and although he has a chance to live in the real world, he actually prefers the chaos, knowing subliminally that the damage of war is far beyond anything the people in the real world will understand. In chaos, his sexuality is perplexing to him, and his intimate connection to his fellow soldiers has led him to a bisexuality he didn't know could exist within him.
The horror of death
The war passages in this novel give a horrifying mask to death. Death doesn't come peacefully in the novel, but with horror and gruesome pain. When death doesn't come, survivors are left with injuries like Hallett's head injury which makes him long for death. The sounds of death are pronounced well in the imagery of the novel, and they are certainly nightmare fuel for any imaginative reader. The horror of death is on full display, culminating in the moment of the protagonist's own demise, a final moment in time where an injury has left him in the sureness of death; he knows for a moment that he will not survive, and this is the ultimate horror.