An energy wave abruptly jolted the USS Enterprise. Spock, the Science Officer, gave Captain Kirk a report that the planet's gravitational pull became nonexistent for a short period, and the space around it "disappeared" for a second. Then, utilizing their sensors, they detected a human being on the planet that had not been there earlier. Spock and Kirk beamed down to the planet and spotted a single-man spacecraft. Lazarus, who was in disarray, plunged off a cliff. Kirk had him transported to the Enterprise for a medical inspection.

Lt. Masters informs Captain Kirk that the perplexing disturbance has exhausted their ship's dilithium crystals in the warp drive. Starfleet has been notified that every area has been affected by this blinking phenomenon and electronic interference. They are apprehensive that it could be a precursor to an assault and have commanded all vessels apart from the Enterprise to vacate the region. Kirk is instructed to discover the source of the disruption.

Lazarus periodically fades in and out of the universe, encountering a lookalike enemy in a "dimensional corridor," creating an energy wink. Spock reports a "rip" in space and time on the planet. Lazarus says his enemy, trying to destroy the universe, is causing the phenomenon.

Lazarus asked Kirk for dilithium crystals to fix his spacecraft so he could keep fighting his adversary. Kirk declined. Lazarus swiped the dilithium from the Enterprise and was apprehended. He denied the pilfering and attributed it to his foe. Kirk beamed back to the planet with Lazarus and safety, forced to look for this enemy. Lazarus had another dimensional corridor episode and was taken back to the infirmary. Lazarus revealed to Kirk that he was a time traveler; his ship was a "dimensional corridor entrance"; the planet below had once been his original homeland. Lazarus declared his enemy had demolished his civilization in the past, for which he had pursued him for hundreds of years.

Kirk is confused by the strange behavior of Lazarus, who goes from being wounded and crazy one moment to being in control and sound of mind the next. Kirk and Spock understand that there must be two different Lazarus - one in this universe, which is not in his right mind, and one in the anti-matter universe, which is. Kirk and Spock hypothesize that Lazarus's adversary is his counterpart from the anti-matter universe. They theorize that both realms will be destroyed if they meet in either the matter or anti-matter universe.

Lazarus escapes from the medical deck and causes a disturbance in engineering to get his hands on some dilithium crystals. After taking the crystals, he beams down to the planet to fix his ship. Kirk follows, but the time machine activates right as he walks into the ship. This causes Kirk to be transported to the anti-matter universe, where he meets the Anti-Lazarus. He confesses stealing the Enterprise's dilithium to stop his counterpart from entering the anti-matter universe through a dimensional corridor. The Anti-Lazarus explains that his people believed there were two universes, but when the matter-counterpart discovered this, he broke down and became determined to destroy his lookalike. He informs Kirk that the only way to spare both universes is to detonate both ships, with both Lazaruses inside, during the "negative magnetic" dimensional corridor that connects the two universes. Kirk states that the destruction of the ships, which are portals, would trap the two Lazaruses in the corridor "throughout time."

Kirk engages with the duplicate Lazarus and shoves him into the interdimensional portal. He returns to the Enterprise and commands that the ship's phasers target the dimension vessel. The two Lazaruses confront each other again while the phaser beams disintegrate the ship/gateway between the universes. Aboard the ship, Kirk ponders that although the universes are preserved "for you and me," the two Lazaruses are eternally confined: "But what of Lazarus... what of Lazarus?"