Formerly like peanut butter and jelly, Nicodemus and Jenner end up being like oil and water—they just don't mix. Nicodemus believes that the rats have to separate from humans and become self-sufficient. Jenner, or the other hand, believes that rats have to be true to their ratliness and should stay "on the margins of human society," stealing (14.23).
Both points-of-view make sense, but we are meant to identify with Nicodemus, whose Plan is nobler than Jenner's. Having Jenner in the story shows both that there is disagreement within the rat community and it makes the reader think about whose viewpoint is the right one. Have you made up your mind yet?