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.

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.

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.

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.

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.

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.

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, 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.

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.

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 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 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.

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.

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.

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 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.

A crew led by Captain Kraspo is searching for the missing Princess Alpha. They bring Will aboard their ship who makes them think the Penny might be there princess, because of this the train Penny to be the future ruler of there planet.

Will is conducting an experiment in a cave and captures a man who claims to be the man who controls time for the entire universe. This ""Time Merchant"" takes Will, Professor Robinson, Smith, and the Robot, to his secret lair. From there, Smith uses the Time Merchant's time machine to return himself to Earth on the day the Robinson's departed, with the objective of NOT sabotaging the Jupiter II mission and letting the Robinsons go on their way to Alpha Centauri. The Time Merchant then announces that if Smith does not get on the Jupiter II, the ship will not fly off course and will therefore be destroyed by a collision with an asteroid several months after liftoff. So Will is sent back to join Smith and try to convince him to get on the Jupiter II as he originally did.

The Robot suddenly announces that the Jupiter II is approaching Alpha Centauri. Everyone is suprised, and the ship lands on a planet, where they are greeted by a group of people who appear to be teenagers from Earth. It turns out that they are aliens who live like Earth-style hippies, and they are incapable of growing old. They want to age normally, and to do this they want to get the older members of the Robinson party to leave in the Jupiter II while the younger members can stay behind and be used in an experiment that will make it possible for them to do so. The aliens trick the older members of the Robinson party into leaving, but Will pulls a fast one on the aliens and the Jupiter II eventually returns to the planet, and Penny, Will, and Dr. Smith, who somehow passed himself off as a young person, are rescued.

Poor Don West is sent to a prison camp.....WITH Dr. Smith!

The galactic showman, Farnum B returns as the producer of the Miss Galaxy Beauty Pageant. They want to Judy to be in the contest, she doesn't want to but Dr. Smith for forges her name and the fun begins.

Dr. Smith disposes of a plant that has grown out of control, but once outside the plant attaches itself to the Jupiter 2. The plant apparently believe that Dr. Smith is its mother, meanwhile the ship is attached by a brave space warrior.

Doctor Smith uses the Space Pod to land on a planet that the Jupiter II is passing by. It turns out that the planet has evolved in such a way that plants are the highest form of life, and some of them are quite intelligent. One of these plants, a large carrot, captures Smith and tries to change him into a plant. The Jupiter II lands and the Robinsons and West come to Smith's rescue, only to be captured themselves. Eventually they thwart the plant creature and make their escape.

The Jupiter 2 lands on a planet which serves as a junkyard. The Robinson's food supply is dwindling. So Dr. Smith tries to sell the robot and the ship in order to get food. Can Dr.Smith be stopped?