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.
Doctor Smith uses the Space Pod to land on a planet that the Jupiter 2 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.
Dr. Smith disposes of a plant that has grown out of control, however, the plant manages to attach itself to the Jupiter 2. The plant apparently believes that Dr. Smith is its mother. Meanwhile, the ship is attacked by a brave space warrior.
The galactic showman, Farnum B, returns as the producer of the Miss Galaxy Beauty Pageant. He wants Judy to be in the contest, but she is not willing. Dr. Smith submits her anyway by forging her name to the contest roster.
Don and Dr. Smith are installing some equipment, when Dr. Smith comes across an alien prison escapee. The prisoner alien makes Dr. Smith change jackets and then runs away. When the prison guards catch up with Dr. Smith and Don, they arrest them for aiding an escape of a prisoner.
The Robot suddenly announces that the Jupiter 2 is approaching Alpha Centauri. Everyone is surprised, 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.
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 2 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 2, the ship will not fly off course and will therefore be destroyed by a collision with an asteroid several months after liftoff.
A crew led by Captain Kraspo is searching for the missing Princess Alpha. They bring Will aboard their ship, and he makes them think the Penny might be the Princess.
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 2 back to Earth. However, Will is not duplicated and attempts to thwart 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.
The Robinsons take in a Princess who is fleeing from a bounty hunter. However, when Will is captured by the bounty hunter, he asks to make a trade of Will for the Princess.
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. When the Robinson's are absent, Dr. Smith decides to turn the ship into a hotel, but he doesn't realize how dangerous his guests are.
A cave boy 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 put on 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 on the Jupiter 2. Meanwhile, the robot meets and falls in love with an 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.
The Robinson's come across a group of space hippies who are trying to destroy the planet the Robinson's currently inhabit. It is 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 Jupiter's 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 2 lands on the planet and rescues them, while 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.
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 is up to Will to stop Dr. Smith.
The Robot is pitted against a supercomputer in an effort to save Don and Dr. Smith.
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.
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.
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, but discover 1947 USA.
The Robinsons have to leave the planet they are on. Once in space, the robot is swept overboard and has to be rescued. While rescuing the robot, the Robinsons find a prison ship filled with cryogenically preserved prisoners.
