Freckles, a little one-armed waif living at the orphanage, has no remembrance of either his father or mother. The butt of the other children's jokes, Freckles finally runs away and after many struggles meets John McLean, the boss of the lumber camp who, admiring the boy's spunk, appoints him watchman of Limberlost, a valuable timber swamp. There Freckles meets Angel, who is spending the summer with the Bird Woman, an enthusiastic naturalist. Angel falls in love with Freckles, but he believes that her feelings for him spring from pity. While they are in the swamp one day, a huge tree topples, imperilling Angel's life. Freckles throws himself in the path of the tree which falls across his chest. Thinking that he is just a waif and therefore unworthy of Angel's love, Freckles does not care to live. As he lies near death, his English grandfather dies, leaving a portion of his estate to his grandson. Solicitors finally trace the lost child to Freckles in the hospital. The news of the good fortune is told to Angel, who goes to tell the dying boy. The realization that he is now on the same social scale with Angel brings back his ebbing life, and the two face a happy life together.