Superboy first encounters the Ciphers during an intense storm that is hammering Smallville. Discovering that the nearby dam has been damaged, Superboy flies onto the scene to prevent a his hometown from being destroyed by a devastating flood. After finding a strange, indestructible parachute caught on the dam, the Boy of Steel repairs the damaged dam with the cloth by tying it down over the gaping hole in the dam, noting that the material of the chute was completely waterproof, not letting a drop of water sieve through it's skin.
Meanwhile, one of the Cipher robots arrives at the Kent residence in Smallville, telling Jonathan and Martha Kent that he is "...your Uncle Cipher...I've come to stay!" Jonathan Kent attempts to call the police regarding the stranger, but is threatened by the being in his home, who uses superhuman strength to crush the his hand just as Clark comes up the stairs from the basement, having just returned home from his dam rescue through the secret entrance in the Kent home. Clark is unable to rescue his foster parents as he used his X-ray vision on the assailant as he entered the house from the basement, finding that the robot is equipped with enough high explosive to blast half of Smallville off the map. "Uncle" Cipher then orders the Kents to stay inside the house.
Clark, using his X-ray vision to watch the stranger in his home while he bandages his father's injured hand, sees the robot communicating to someone in a cryptic digital code. Clark, rushes off to his basement laboratory, but is stopped by Cipher, who reminds the teen that he will be watching him, after Clark uses the excuse that he has homework to do.
Working in his basement lab, the only portion of the house that is actually safe from Cipher's prying eyes due to it being sheathed in lead, Clark begins to put the pieces of the puzzle before him together, noting that the robot's skin was made from the same indestructible material as the parachute he found at the dam, and that the digital code that the robot was communicating with was actually a simple numbered alphabet sequence from 1 to 26. Clark, uncovering the invasion plot, then switches to his Superboy identity.
Sneaking out of the Kent house through the secret entrance, Superboy quickly collects the materials to construct a bomb-proof room in the basement, and then lures "Uncle" Cipher downstairs. A small battle is waged between the superhero and the robot, until the robot suddenly shuts down while holding Superboy's indestructible body over his head. Investigating the robot's prone form, Superboy is hit with Kryptonite beams from the robots eyes, which renders him unconscious. The robot then returns to the upstairs unders Cyber's orders.
During scuffle between Cipher and Superboy, Lana Lang stops by the house for a pre-planned dinner invitation, and the recovered Cipher tells Martha to go ahead with the dinner party. During a conversation with Lana, the Kents learn that Lana also has a "visiting relative" staying at the Lang home. Martha, not knowing that her son has been rendered unconscious in his Superboy costume in the basement, tells Lana to fetch Clark for dinner. As Lana begins to go down the stairs into the basement, the Boy of Steel quickly recovers from the Kryptonite poisoning due to the intervention of some chemicals that were knocked over during the fight with Cipher and accidentally combine to provide a temporary antidote. Switching back to Clark, and ordering one of his Superboy Robots to lie in a prone position in case "Uncle" Cipher should check on the condition of his prey, the hero exits the house at super-speed and re-enters the house through his bedroom window and calls Lana out of the basement to protect his secret identity.
Exiting the basement, Lana sneaks a peek at the "visiting relative", and, upon seeing Cipher, runs from the house. Lana had hoped that the Kents would be able to help her as she too had an "Uncle" Cipher in her home, a fact that the Cipher in the Kent home confirms, stating "Ah, yes...Cipher 5...assigned to her house! As my other cohorts have been to families thoughout Smallville!"
During dinner, Clark begins to run through the events of the evening. Realizing that the reason that the robot shut down during their battle was because Superboy's invulnerable body blocked out the power signals being sent to the robot by Cyber. Using this knowledge to his advantage, Clark, having walked Lana home and switching to Superboy after dinner, launches himself into the sky and traces the robot's power source to an alien ship in orbit piloted by Cyber. When Superboy attempts to apprehend the alien's ship, the scientist types on computer screen a message in his digital code, "Any contact on my craft...and...instantly...every 'Uncle' Cipher in Smallville will be triggered by an energy-pulse...and blow your town off the map!"
During this confrontation with the alien, Lana runs from her house, unable to take this invasion any longer. With the Boy of Steel temporarily stymied as to what to do, Cyber sends a signal down to Earth, activating two of his Ciphers, Cipher 1 from the Kent house and Cipher 5 from the Lang house, with orders to destroy any who stand in their way, starting with Lana. Seeing the girl in trouble, Superboy zooms back to Earth, rescuing her in the nick of time. Flying the Lana to the Smallville Reservoir, Superboy exhales a gust of super-breath, freezing the contents of the reservoir into a solid block of ice, which he uses as a shield as he flies back to Cyber's ship. The shield's reflective surface blocks out the signals that the villain has been sending to power and control his robots, effectively deactivating them as a power surge causes Cyber's ship to self destruct, apparently killing the villain (SB No. 150/1, Sept 1968: "The Stranger Who Stalks Smallville!").