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 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.

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.

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.