Ykhjuy

I was wondering about this after I realised that Dr. Isaacs in Resident Evil wants to wipe out humanity again and then restart it with a chosen few so life stands a better chance.

Dr. Isaacs: I propose that we end the world... But on our terms. An orchestrated apocalypse. One that would cleanse the world of its' population but leave its infrastracture and resources intact. It's been done once before. With great success. The chosen few will ride out the storm, not in an ark as in the book of Genesis, but in safety. Underground. And when it's over, We will emerge onto a cleansed Earth. One we can then reboot. In our image.

_{Resident Evil: The Final Chapter}

And that Thanos from Marvel has a similar idea but on a universal scale. I know that his motivations aren't the same in the original The Infinity Gauntlet comics but in the MCU and specifically Avengers: Infinity War he wants to do it so life can succeed.

Thanos: Little one, it's a simple calculus. This universe is finite, its resources finite. If life is left unchecked, life will cease to exist. It needs correction.

_{Avengers: Infinity War}

But, what was the first work which brought about the idea of deliberately wiping out half of humanity, a species, life, a planet, a universe in order for it to survive?

1950: "The New Reality", a novelette by Charles L. Harness, first published in Thrilling Wonder Stories, December 1950, available at the Internet Archive.

Professor Luce, a mad ontologist, constructs a device with which he intents to reset reality, expecting that only a select few (himself included of course) will survive.

Prentiss drew deeply on his pipe.

"I saw it."

"Did you understand it?"

"No. It wasn't all there. At least, the apparatus on the table was incomplete. There's more to it than a Nicol prism and a goniometer."

"Ah, you are clever! Yes, I was wise in not permitting you to remain very long — no longer than necessary to whet your curiosity. Look, then! I offer you a partnership. Check my data and apparatus; in return you may be present when I run the experiment. We will attain enlightenment together. We will know all things. We will be gods!"

"And what about two billion other human beings?" said Prentiss, pressing softly at his shoulder holster.

The professor smiled faintly. "Their lunacy — assuming they continue to exist at all — may become slightly more pronounced, of course. But why worry about them?" The wolf-lip curled further. "Don’t expect me to believe this aura of altruism, Mr. Prentiss-Rogers. I think you're afraid to face what lies behind our so-called 'reality.'"

[. . . .]

He knew in a brief flash of insight, that for sentient, thinking beings, Time
had suddenly become a barricade rather than an endless road.

The exploding bomb — the caving cottage walls — were hanging, somewhere, frozen fast in an immutable, eternal stasis.

Luce had separated this fleeting unseen dimension from the creatures and things that had flowed along it. There is no existence without change along a temporal continuum. And now the continuum had been shattered.

Was this, then the fate of all tangible things — of all humanity?

Were none of them — not even the two or three who understod advanced ontology, to — get through?

[. . . .]

She'd got through!

The whole world, and just the two of them!

His heart was pounding ecstatically as he began to run lithely upwind.

And they’d keep it this way, simple and sweet, forever, and their children
after them. To hell with science and progress! (Well, within practical limits, of course.)

As he ran, there rippled about his quivering nostrils the seductive scent of
apple blossoms.

Probably not the first, but:

1964. In Stanley Kubrick's movie Dr. Strangelove, towards the end, with impending nuclear war in sight, the titular character suggests gathering a few hundred thousand selected people (including, of course, top politicians and military personnel) underground to wait for the surface to become habitable again, repopulating the planet. He suggests a 10:1 female/male ratio for faster breeding - which isn't rational in my opinion, since it would probably take several generations before the surface becomes habitable again and you don't want the underground habitat to become overpopulated. But of course, the outlook of having access to plenty of women helps persuade the decision-makers to adopt the plan.