Raised since infancy in a Chicago orphanage, he speaks with a slight Irish accent, "scarcely definite enough to be called a brogue."
Exhausted after days of walking and looking like a hobo, he applies for a job with the Grand Rapids lumber company, guarding timber in the Limberlost Swamp.
McLean, part owner, organizer and field manager of the large company, and enthralled with the Limberlost, is impressed by the boy's polite assertiveness and hires him despite his youth and disability.
Freckles' duty is to twice a day walk the perimeter of the lumber company's land, a seven-mile trek through lonely swampland, and to be on the watch for those who aim to steal the expensive timber.
McLean's chief worry is Black Jack Carter, who has sworn to smuggle several priceless trees out of the swamp.
Freckles' weapons are limited to a revolver and a stout stick which he carries at all times and uses to test the wire that marks the company's boundaries.
Initially terrified of the wilderness after a lifetime in an urban environment, Freckles first conquers his fears, aided by exploration of the Limberlost during its barrenness in the severe winter, and feeds the fickle birds ("my chickens" he calls them) that had once frightened him.
The next afternoon, while he is reading in his room in the swamp, recovering from his beating and taking refuge from the heat of the day, a lovely girl about sixteen years of age appears looking for him.
The next day he returns the Angel's hat that she left behind during the fracas to her father at work, rather than going to her home, and this gentlemanly behavior makes a positive impression.
However, the Swamp Angel finds them, pretends to think they are on official camp business, flirts with Black Jack to make him trust her, and rides off on Freckles' bicycle.
When the reinforcements return, led by the Angel, they find that the Bird Woman has shot Black Jack in the arm and captured both him and Wessner.
The fallen logs are recovered but Black Jack has sworn revenge on Freckles and the Swamp Angel, and a thorough search of the Limberlost fails to find him.
They prove themselves to be kind and noble, and explain that Freckles' father had been disinherited when he married a clergyman's daughter, and both had perished in the fire that took his hand.
Rather than go to Ireland and live as a lord, he will go to college in the United States and then join McLean in managing the lumber company, so that he can always be near the Limberlost.