Junior is a movie that asks the question what if a man has a baby. The story revolves around two doctors Dr. Alexander Hesse and Dr. Larry Arbogast who have invented a fertility drug called "Expectane", it supposed to limit the chance of a woman to miscarry. They bring theirs findings to the Food and Drug Administration who turn them down, due to the fact that they cannot test the drug on women. In response to the FDA review the program is shut down. Arbogast talks Hesse into testing the drug on himself.
Larry unable to find an unwanted embryo he breaks into the lab and takes one from Dr. Diana Reddin who is over the lab now. Arbogast implants the embryo inside Hesse. As this is going on Larry is also dealing with that fact his ex wife is also pregnant by someone else.
After a while Alexander hormones are out of whack so Larry decides to cut the experiment short. Hesse who is now bounding with the baby goes home and decides to continue on taking the medicine.
Alexander goes on covering up the fact that he still taking the drug. Larry finally finds out and is upset, he moves Hesse in with him so that he can keep a watch over him and the baby. One night out with Reddin she states that she has frozen one of her eggs and called it Junior. Shocked at the news Hesse heads back to Arbogast house to confront him. Dr. Arbogast admitted that he took it from Dr. Reddin inventory, Hesse tells him that it is hers personality.
Eventually, Hesse goes into labor Larry delivers his baby by caesarean section. Hesse and Diana names the baby Junior. The movie ends with the two couple on the beach celebrating. the birthdays of Junior and Jake the camera focus on Diana it is showed that she is pregnant.