The poem begins with the speaker, a farmer, discovering a mouse after accidentally destroying its nest while plowing. He observes the mouse's obvious fear, noting its hammering heart and its attempt to run away, but tells the mouse not to be afraid. He assures it that he won't try to hurt it. In fact, he thinks, it's regrettable that mice and other animals are so afraid of humans, even if it's completely reasonable for them to be scared. Humans have such dominance over the natural world that, unfortunately, mice have every reason to be scared. Yet the speaker feels that he has more in common with the mouse than most people realize, and has no desire to hurt it.
He thinks about the fact that mice are known to steal grain and crops, but tells the mouse that it's an understandable thing to do. It's natural for the mouse to steal in order to survive, while humans are unlikely to even notice if a small amount of food goes missing. The farmer turns his attention from the mouse's need for food to its need for shelter, observing sadly that he has wrecked its nest. He imagines out loud how hard the mouse must have worked chewing on sticks and stems to make a nest, which is now gone, its walls blowing in the wind. In fact, the farmer frets, it's about to get even colder as winter approaches, and the mouse badly needed the shelter of its nest.
However, he tells the mouse, it's not alone—for humans and mice alike, even the most meticulous plans often don't work out, leading to heartbreak instead of the expected happiness. In fact, the speaker says, the mouse is actually lucky compared to him, because its mental life is limited to the present, meaning that it doesn't have the capacity for anxiety or regret. The speaker, with his human abilities to think about the past and future, deals with both grief about the past and fear for the future.