Gilligan rescues a robot named Wizzard from a landslide, which then grants Gilligan's every wish out of gratitude. Eventually, Mr. Howell becomes the robot's master, and misuses his wishes, ruining another chance to get home.
The Skipper has been shirking his duties at the compound, and insists that his time is better spent guarding everyone from alien invaders, though in reality, he is simply napping. When real aliens invade, he is quickly captured, and must be rescued by his "helpless" friends.
The Skipper becomes despondent due to having been away from the sea and his boat for so long, so the others decide to build him a small boat, which serves the dual purpose of allowing the Professor to reach a small island which he thinks might be a source of mica, needed to repair their rocket. An attack by a sea monster leaves them stranded on the island, but not all is as it appears...
Gilligan continually attempts to avoid his chores to read his comic book, causing a series of mishaps and accidents, culminating in the castaways falling into a hole that leads to the center of the planet, where they are taken prisoner.
While collecting samples from the Million Lakes region of the planet for the Professor, Gilligan accidentally falls into a lake full of yellow liquid and becomes a giant. Space circus owner P.C. Barnaby arrives on the planet in his ship, and tries to steal Gilligan and turn him into his latest attraction.
Bumper continually gets scolded in his attempts to find someone to play with. He decides to run away, and gets abducted by visiting aliens who worship his species.
The Professor discovers that the planet on which they are marooned will soon be pulled into a "space hole", so the castaways try everything they can to avert this disaster, including mounting the rocket pod from their ship on a tower to try to change the planet's course.
Gilligan and Skipper find a cloning device that Gilligan accidentally walks through twice, and Mr. Howell and Ginger go through once, creating multiple copies of themselves with disastrous results. Eventually Bumper coaxes them all to run through the device multiple times until it short circuits and explodes, causing all the clones to vanish.
Gilligan discovers a treasure trove of advanced technical equipment, including a "size transformer cube", and accidentally shrinks all the castaways except the Professor. Soon after, pirates arrive looking for the cube and the other equipment, and chaos ensues...
While trying to retrieve a wrench that fell down a hole near their rocket, Gilligan discovers a map leading to a spaceship called The Lost Barque. The castaways head to a nearby cave to search for it, unaware that a group of tiny aliens who call themselves Quarks are trying to stop them so they can find the ship first.
Gilligan accidentally turns on the Professor's radio and attracts a pilotless space probe. One of the castaways might be able to pilot it back to earth, but the castaways all want the fame and fortune, so the Professor puts Bumper in charge of training them to see who is best suited.
A cosmic hurricane damages the compound, and the rocket's steering mechanism is blown away. While searching for it, Gilligan stumbles into a cave where an old man mistakes him for a great hero, and gives him a cape which grants superpowers, so he can defeat a villain named Gooniack.
An alien drill sergeant (who resembles Darth Vader) and his commanding officer (who resembles Groucho Marx) land on the planet, and mistake the castaways for a group of recruits that they have been sent to train for intergalactic space missions.
