Nate had forgotten to reply to Lara's confession. His mind was broken, and he didn't say anything while hugging her like a bear.
Then, when he remembered, it was late, and they had to go. The atmosphere was gone, and he had to accept that he was a failure as a lover. In many ways.
He had started that war, and he had to finish it. Yet, he hated his decisions at that moment: if not for it, he would still be cuddling with Lara, telling her how much he had loved her since the start and how often he had thought of her. Moreover, his feelings had become more stable and grew in intensity since the moment she had reappeared. They had transformed from something purely instinctive to a rational emotion. He knew what he wanted, and he wanted to want it.
Still, duty called.
At the same time, he was grateful that the conflict had made Lara say those words to him. Even if she might be taking them back soon, he had a few hours to live as her beloved.