The Space Pod lands on a planet that is inhabited by creatures who all look alike, and aspire to be different. They capture the Robinsons and make duplicates of them with the objective of using the duplicates to fly the Jupiter II back to Earth. Will is not duplicated, and he thwarts their plan.

Professor Robinson is caught in a matter transfer emission ray, and subsequently ends up in another dimension where he is confronted by a version of himself and Don. However this realm is the opposite of his own dimension, the anti-matter world, where everything in reality is twisted. The evil John returns to the family and attempts to take over the Robinsons and take over John's life. Will he get away with it, or are Will and the Robot able to defeat him, and restore the world to it's natural order.

The Robinsons take in a Princess who is fleeing from a bounty hunter. Will is captured by the bounty hunter, who wants to trade the boy for the princess. the robot then comes up with a idea to save the day.

Two aliens, who are actually intergalactic bank robbers, transform themselves into Earthlings. They revive a man named Zumdish who operates a tour agency and they pretend to be his clients. The Robinson's head off and Dr. Smith is left alone, Smith's decides to turn the ship into a hotel and doesn't realize how dangerous his guests are.

A caveboy appears and attempts to lure Penny away, but she refuses, and is instead caught in a net. She is transported to an intergalactic zoo, were she will be puton show, meanwhile Dr. Smith tries to take over the zoo.

The Robinsons encounter two Aliens who are on a mission to seek and destroy an escaped Robot Prisoner, whom they believe to be hiding at the Jupiter Two. Meanwhile, the Robot meets and falls in love with this evil, female Robot. She tries to turn the Robot bad, but ultimately, is defeated by the Robot and the Robinsons, but not before wreaking havoc over the planet.

A strange blue fog seems to be engulfing the Jupiter 2 periodically. Dr Smith and Will commment seperately that they want to be left alone. When the members of the Jupiter 2 begin to randomly disappear as the fog comes, Dr Smith thinks he is to blame. Eventually Will discovers a strange creature which takes over Dr Smith. The creature tells Will that he is his own Id. Will finds out his Id is a creature he created full of Will's own personal demons, thoughts, feelings and insecurities. Will defeats the creature by overcoming his ""fears"" and throws the powerless creature in the power core. The members of his family are returned.

The Robinson's come across a group of space hippies who are trying to destroy the planet the Robinson's currently inhabit. Up up to the Robinson's and Dr. Smith to stop them or they will all be doomed.

Dr. Smith, Will, and the Robot are accidentally launched in the Space Pod. They land on a planet that is controlled by an alien machine that creates illusions to confuse visitors and drive them away. The Jupiter II lands and rescues them, and the robot destroys the alien machine.

Before leaving their planet, the Robinsons meet a boy alien called J-5. They take him with them to return him to his home planet. They meet a strange ship, which turns out to be an earth ""lighthouse"" for lost ships. Thinking this ship will help them with extra fuel and star charts they celebrate, however when J-5 learns that they don't have enough fuel to take him home, he angrily sets about to destroy them all with a creation of his imagination. J-5 begins a new life at the lighthouse, and the Robinson's leave in the knowledge he will be looked after by the kindly, old lighthousekeeper.

Dr. Smith and the Robot are exploring a cave. Smith pushes several buttons on a conspicuous control panel. The buttons activate a cyborg creating device. It up to Will to stop Dr. Smith.

The primitive beings are actually wards of a computer, Protinius, which can confer temporary advanced sentience on the leading man in order to communicate Protinius' will. The episode also features a temporary camaraderie between Don and Smith, a burying of the hatchet, when Don is rescued by Smith from a pit, and then says ""Doctor Smith"" - using the word Doctor for the first time unknown ages. However, their camaraderie dissolves and the characters are back to ""normal"". Not the first time Smith has become selfless and a man of some integrity, but as usual, Smith returns to normal.

In an episode reminiscent of the first season episode "The Challenge", Professor Robinson and the Robot land the Space Pod on a planet, and Professor Robinson kills an attacking monster, only to discover that he has interfered with a contest where a highly intelligent alien who aspires to rule his home planet is being judged on how well he hunts. The alien forces Professor Robinson to take the role of one of the hunted animals in the contest, allowing the Professor one weapon. The weapon has a defect that imperils Professor Robinson, but the Professor outwits the alien and survives the ordeal.

Dr. Smith answers a distress call from an alien space ship. He arrives there using the Space Pod, and discovers that the aliens want him to operate on (actually, repair), their leader. It turns out that the aliens are a race of some sort of robot that survive as long as their leader, who functions as their central control timepiece, is in working order. The Robinsons come to Smith's rescue in the Jupiter II. The leader is repaired by the robot, and the extended space family Robinson leave the alien space ship safely.

The Jupiter 2 and all aboard are caught in a space 'time-warp'! After everything seems to return to normal, they're shocked to find Earth within their reach and decide to return home. Though they're perplexed that they are unable to contact 'Alpha-Control', they decide to land in the 'good ole USA' ....only to find it's 1947! As usual, Dr. Smith causes issues & even considers staying behind when the Robinsons and West announce plans to leave.

The beginning of the third season finds the Robinsons having to quickly leave the planet they are on, which is a similar plot to the beginning of the second season. Once in space, the robot is swept overboard and has to be rescued. Then the Robinsons find a prison ship filled with cryogenically preserved prisoners. The prisoners have been interred past their normal sentences due to a malfunctioning timepiece on the prison ship. Professor Robinson repairs the timepiece and frees the prisoners. Robby the Robot makes another appearance, threatening Professor Robinson and Major West.