Mr. Howell tricks the other castaways (except the Professor) into building him a private beach club with the promise of membership, but upon completion, he decides that they are not qualified to join. Lovey and he soon grow bored by themselves, and when a typhoon destroys their club, they are forced to re-evaluate their snobbery.
A geological sampling robot, launched from Cape Kennedy, and meant to explore other planets, ends up crashing on the island. With the Professor busy on the other side of the island, the other castaways become convinced that the robot is an alien, and soon let their prejudices about the "alien" and each other cause havoc. When the Professor returns and explains things to them, they realize that the robot could end up saving them, and that they had been bigoted toward it the whole time.
Famous explorer Lars Hyerback arrives on the island, and finds the castaways, and they believe rescue is at hand, but unfortunately, Lars is such an egotistical scatterbrain that he cannot remember where his boat is. Meanwhile, the Professor's seismic equipment falsely indicates an incoming disaster, adding to the chaos.
The Skipper misunderstands a conversation, and believes Mary Ann is in love with Gilligan, so he sets about to turn Gilligan into a real man. This eventually leads to Gilligan accidentally saving the Howells' lives, and they then adopt Gilligan as their son. Mr. Howell then proceeds to try to turn Gilligan into G. Howell, the first, but is almost too successful, and Gilligan becomes a snob, too good for anyone.
Ginger begins to feel unappreciated, and after overhearing the Professor explaining ESP, decides to pretend she has the ability to see the future. This backfires, and the castaways decide she is a liar who cannot be trusted. Meanwhile, a trunk full of magic gear washes up on one part of the island, and a pair of escaped convicts washes up on another. Gilligan decides he wants to put on a show for everyone, while Ginger tries in vain to convince everyone that she has seen the convicts and their boat.
Mr. Howell hears a story on the radio that leads him to believe lead will soon be more valuable than gold, so he lies to Gilligan to get his help in mining it. Meanwhile, a whaling boat washes ashore, and the rest of the castaways work on getting it seaworthy, unaware that Mr. Howell's lead stockpile will soon ruin their plans.
Gilligan has a dream about a mysterious stranger who teaches him how to turn the radio into a transmitter, so the castaways can send a rescue message. Everyone gets so involved in trying to get Gilligan to remember his dream, they do not notice an actual mystetious stranger is on the island, spying on them.
Tired of seeing his fellow castaways becoming apathetic about their daily chores, the Skipper begins bullying everyone into action. While out searching for food, Gilligan is kissed by a strange flower, which gives him super powers. The other castaways enlist Gilligan's help to end the Skipper's bullying, unaware that they should be using his powers to try to escape the island.
Mr. Howell decides that he wants to build a resort on the island, so that once rescued, he can add to his fortune. The other castaways are initially skeptical until he butters them up with promises of lucrative positions once the resort is open. While working on the resort, Gilligan digs up a boat, but shortly thereafter it is found in pieces, leading to suspicion among the castaways.
Gilligan and Snubby find a crate full of old naval movie equipment, and the castaways decide it would be fun to make a film. They get so busy arguing over what it should be about, and who the star is, that they ignore Snubby, that repeatedly tries to show them a film with instructions on how to build a rescue boat.
With typhoon season approaching, the Professor draws up plans for a train, and tracks leading to a cave, so the castaways can get to shelter quickly and safely. No one follows his plans properly, however, leading to chaos when an actual typhoon approaches, and Mr. Howell steals the train to ferry his valuables to safety first.
The Professor's instruments predict prolonged drought, and with food supplies dwindling, the castaways decide to build an irrigation system and start a farm. Mr. Howell cheats, though, using the Professor's photo-enlarging fluid as fertilizer. The others discover this, and begin doing it, too, resulting in giant, but inedible, crops.
Original series bumpers.