When the rocket launch for a space mission goes awry, its astronaut, Captain Anthony Nelson, finds himself stranded on a desert island. There, he finds a beautiful antique bottle lying there on the sand. When Tony opens the bottle, he is shocked to find a beautiful, 2,000 year old genie named Jeannie, who is now calling him her new Master and willing to grant him anything he wishes.
Jeannie blinks Tony to ancient Persia, where he avenges Jeannie's honor against Ali, the Killer of Giants. Meanwhile, Jeannie visits her parents and happily announces that she has found the man she wishes to marry, her Master, Tony Nelson, a man who "makes his living flying through space."
Tony has forbidden Jeannie to interfere while he and Roger are on a week long mission under simulated lunar conditions. But, Jeannie decides to go along anyway, hidden in Tony's canteen.
General Stone is leaving the US Air Force to accept an ambassadorship overseas. He offers Tony the opportunity to come along and be his Military Attache. General Stone's daughter, Melissa, who is also Tony's fiancee, urges Tony to accept the prestigious position and move up their wedding date.
Jeannie joins the WAFs in the hope of being assigned Tony's secretary, but she is ordered to report to another post.
During a cruise, several people overhear an argument between Tony and an unidentified woman, Jeannie, but when they investigate, the woman is nowhere to be found.
Jeannie wants Tony to quit the astronaut program because it's too dangerous, especially since he refused to let her help when he takes scheduled walk in space.
Jeannie feels that Tony is taking her for granted, so she stops using her magic powers and starts acting like a normal female.
Tony is in Hollywood working as a technical advisor on an astronaut movie. Jeannie plans to keep an eye on him.
When Jeannie finds out that Tony's interested in the desalinization of sea water, she conjurs up her Grandfather Bilejik.
An 8 year old boy, Custer, idolizes Tony. One day when making an unannounced visit, Custer sees Jeannie's magic at work. The little boy tells almost immediately. Dr. Bellows learns about this and decides to use him to prove that the recent weird events with Tony have some explanation. Of course, Jeannie uses her magic to cause even more trouble.