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.
Gilligan and the Skipper discover a pirate's treasure chest, and the other castaways all fight over the gold inside. They soon come to believe a pirate ghost is after them, and become paranoid. The Professor uses Gilligan and some glowing paint to trick them and bring them back to their senses.
The castaways begin to notice that many of their personal possessions are missing, and start accusing one another of being the thief, unaware that the actual culprit is a raven.
The castaways decide that life on the island is too chaotic, and that better leadership is needed. After a long series of arguments and an election, they end up with Gilligan as president.
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.
Ginger feels her acting career is over, because she has been trapped on the island for so long. The other castaways decide to pretend they are filming a TV special to raise her spirits, unaware that the fake camera Gilligan builds is actually transmitting signals to a nearby aircraft carrier.
The castaways, feeling lazy, force all their chores upon Gilligan, but when they eat the dessert he prepares for them after dinner (using strange beans he found on the other side of the island), they all revert to a childlike mentality, leaving Gilligan stumped as to how to change them back.
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 castaways are all craving some solitude, and they decide to live on their own, leaving Gilligan confused and alone at the compound, with only various animals for company. Things get more complicated when Gilligan digs up an old hot air balloon.
The Professor determines that the island will sink in 25,000 years, but the rest of the castaways mistake the disaster as being imminent. The Skipper builds a raft, and they hold an athletic contest to determine who will command the vessel.
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.
After a misunderstanding involving a lion, the other castaways are convinced they have to teach Gilligan to be more brave. Their plans repeatedly backfire, but eventually they learn being a man is more than heroics.
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.
While flying a toy airplane, Gilligan causes the Professor to hit his head, and he develops amnesia. While only temporary, this ends up being a serious problem when Gilligan discovers the wreckage of a real plane in the jungle, because the Professor is the only one who knows how to fly it.
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.
Frustration with the animals on the island (especially Gilligan's new elephant friend) leads the castaways to attempt relocate them to the other side of the island. Meanwhile, two jewel thieves show up on the island, looking for a place to temporarily hide a priceless gem.
Dissatisfaction with the island car leads the castaways to fixing it up, but afterwards they cannot decide whose turn it is to use it. They solve the problem by all building their own cars, leading to traffic and chaos, and eventually the island's first courtroom trial.
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.
A series of practical jokes leads to the Skipper and Mr. Howell refusing to talk to one another. Their feuding complicates the Professor's plan to build a radio tower to help them communicate with a satellite scheduled to fly over the island.
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.
