That really depends on the identification of the polyisocyanate and the prepolymer. It might be a tri- or tetraisocyanate, which would, as Honclbrif said, provide crosslinks that tie your polymer chains together into nets. It might also contain groups with different properties between the isocyanates, such as a highly hydrophobic segment in a mostly hydrophilic polymer or vice versa, or possibly a highly crystalline region in a mostly non-crystalline polymer or vice versa, to change other properties of the polymer. Or if your prepolymer has very long segments, it may simply be a very small segment added to provide more rapid reaction and curing of your prepolymer.