Sound Familiar?

In standard orbit around an iron-silica-type uncharted planet, the USS Enterprise prepares to complete its survey, when everything within sensor range suddenly "blinks", almost as if the universe is on the verge of ceasing to exist. And, in the wake of this, a man appears on the surface of the planet, where moments earlier there was no life.

Beaming down, Captain Kirk, Spock, and the landing party encounter a man. Dirty, and disheveled, he falls from a rock. The landing party returns to the Enterprise with him, where Kirk learns more news – the strange phenomena drained the dilithium crystals almost completely. Still worse, Starfleet issues a Code Factor 1 message – invasion status. The effect experienced by the Enterprise was also experienced everywhere in the galaxy, and far beyond. Starfleet withdraws all nearby ships – Kirk and Enterprise are the bait.

Kirk talks to his "guest" – a man named Lazarus, who is pursuing a "thing", a monster who destroyed his entire civilization. Beaming down, Kirk learns from Spock that there is no other creature here. Accusing Lazarus of lying, Kirk demands the truth – and the universe turns inside out. The same "winking" phenomenon occurs again. And Lazarus... first he has a bandaged forehead, and then he doesn't, and then he does again.

Meanwhile, Spock has discovered a source of radiation that is not there – a "rip" in the universe, where regular physical laws do not apply. The key to locating this source seems to be the dilithium crystals – a revelation which excites Lazarus, who demands the impossible: that Kirk give him the crystals.

The captain refuses, but Lazarus overpowers two engineering officers and steals two crystals, nevertheless.

Kirk confronts him, but he denies it, blaming his monster. And the evidence suggests he isn't the thief, for the crystals are not aboard his ship. Back aboard the Enterprise, Kirk confronts Lazarus with his lies, and learns that Lazarus distorted a fact: he is a time traveler. The dead world Enterprise orbits is the distant future of his destroyed homeworld; the place and time he has traveled to in pursuit of the monster.

Speculating, Kirk and Spock conclude that the strange energy must come from a source outside the universe. A source in another universe. There are two copies of Lazarus, and they are periodically exchanging places through a kind of door – and if they ever exist in the same universe at the same time, everything, everywhere, will be annihilated in a cataclysmic matter/antimatter explosion.

Meanwhile, the alternative Lazarus steal the ship's energy crystals, then beams down. Kirk pursues. As he attempts to enter Lazarus' spaceship, he vanishes, hurled through the corridor into the other universe.

Once there, he meets the other Lazarus, the sane Lazarus, and learns the truth. Anti-Lazarus' people discovered how to pass through the negative magnetic corridor that both connects and protects the two universes. When this happened, Lazarus couldn't bear the knowledge that he had a duplicate, and resolved to destroy his other. He is mad and doesn't care if this causes the death of two universes. Anti-Lazarus and Kirk realize he must be stopped: if Kirk can force Lazarus into the corridor, Anti-Lazarus can hold him there, and Kirk can destroy his spaceship – which will also destroy Anti-Lazarus' spaceship. Access to the corridor will be sealed forever, and both universes will be safe. And two men named Lazarus will be at each others' throats for the remainder of eternity. Kirk goes back through the corridor and in a hand to hand combat throws Lazarus into the corridor. Back on board Kirk orders the Enterprise to fire phasers at the time ship which then disappears in both universes; both Lazarus are trapped forever in the corridor and both universes are saved.