Fighting off a cold, Jay inadvertently swallows an alien embryo thinking it's a vitamin. Now he's pregnant, and to compound matters, the real mother, known as a Bobbalot becomes Jay's shadow, following him everywhere to ensure her unborn child's well being. Meanwhile, Jay and Kay are after the Fmecks who are stealing some of New York’s most famous landmarks with the aid of a Shrink Ray, which reduces each structure to a fraction of its normal size. While on stake out, Elle gets trapped inside the Statue of Liberty when it is shrunk by the Fmecks. Not good news for Jay, since Elle is the only one who can deliver the baby without it exploding out of Jay's chest. With Jay and the baby Bobbalot's life hanging in the balance, the action culminates at Coney Island, where the MiB get the drop of the pesky Fmecks. Elle is resized and delivers the alien baby just in time to help thwart the Fmecks. In the end, Jay takes on the role of the proud papa.