Kipper shows up on Willbury's doorstep as a "smiling man with a platform made of sticks fixed to his head" (15.26). On the platform stands Tom, the rat he describes as "'the boss'" (15.31). Kipper doesn't seem to mind that he's "'just the muscle around here'" (15.31), which is good since he does a lot of muscular things throughout the story. He pedals Grandfather's contraption that animates the doll to get Arthur the keys to his dungeon cell, for instance, and he carries boxtrolls through the flooded caverns underground.
Kipper has good intentions, plus he's not a total blockhead, either, since he's the one who comes up with the idea to disguise everyone as boxtrolls so that they can sneak by the police (34.44). He also decides to give Arthur a tiny model of the Ratbridge Nautical Laundry that he had been making: "'when he heard that you had lost all your toys, he decided you would make a good home for it'" (54.78). That's sweet, huh? We think so, anyway.
Kipper shows a surprising solidarity with the boxtrolls, helping them out throughout the story and eventually learning to speak their language. It's a heart-warming instance of inter-species affection, and it makes him "very happy" (55.1). So he might be the muscles of any given situation, but Kipper still gets a happy ending.