The Doctor had never heard of a race like Bill described, but that wasn't too unusual. The universe was often surprising him with races and creatures that he hadn't encountered before - it made traveling around in his TARDIS worth while.
The sound of a bacteria escaping to destroy the planet was disturbing, but then he blurted out, "Oh! The fire would be fueled by the ethanol and purge the bacteria. That is very clever of me to think of that." He couldn't help himself, but he noted that Bill wasn't amused or impressed, so he swallowed his smile and pride to fall silent again.
The main thing the Doctor got out of Bill's story was the part about love. Bill had bargained for his life with the Monks out of love.
Sitting back and threading his fingers together, holding them thoughtfully against his mouth, he considered what Bill had said. "And that's where you were brought in. After you'd made the deal." He thought for a moment more. "You did what you thought was right. You bought the Earth some time. Nothing is irreversible, I'm sure there's a way to stop the Monks. There always is."