Commodore Matt Decker eventually explains that the USS Constellation encountered a massive planet-killing machine, which damaged their ship when they tried to destroy it. Decker evacuated his crew to a nearby planet, but the doomsday machine soon destroyed the planet and the Constellation's entire crew with it. After transferring over to the Enterprise, Decker steals a shuttlecraft and flies into the machine in a suicide run. This gives Kirk the idea to explode the Constellation inside the planet killer. Kirk's plan destroys the machine's power system, leaving it dead in space, and the planet killer never appears onscreen again.
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Upon studying the planet killer, Spock (Leonard Nimoy) determines that the machine is automated and self-sustaining as long as it has planets to consume. Spock also concludes that the machine originated from outside of the Milky Way galaxy, and will cut through many more populated worlds if it continues on its course. Captain Kirk surmises that the doomsday machine may have been created by an alien race as a bluff in some long-forgotten war. Because the neutronium hull of the machine is nearly indestructible, Kirk realizes that the only way to destroy it is from the inside out.
When the Constellation's weapons detonate inside the machine, it leaves the now inert planet killer floating in space. Considering how much remains unknown about the doomsday machine, it seems likely that Starfleet would wish to continue studying it. They have no way of knowing if the machine has some kind of ability to repair itself or if its presence in space will cause other problems. Kirk and Spock even speculate at the end of the classic Star Trek episode that there could be other doomsday machines out there, but this thread is never followed up on either.
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A model of the planet killer can be seen at a bar at Starbase 25 in Star Trek: Lower Decks season 2, episode 5, "An Embarrassment Of Dooplers."
The Star Trek: The Next Generation tie-in novel Vendetta by Peter David features a similar device that was believed to have been created as a weapon to combat the Borg. Several Star Trek short stories, comics, and video games have also featured versions of the planet killer, some of them direct continuations of "The Doomsday Machine," while others have incorporated different kinds of planet-killing machines. As far as the official Star Trek canon is concerned, however, the fate of the doomsday machine Captain Kirk encountered on Star Trek: The Original Series remains a mystery.