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Assume that 'Oumuamua was a Von Neumann Berserker, which, at the detection of civilization, triggered a bomb that exploded at lightspeed.
From the perspective of Earth, due to the speed of the explosion, nobody could even notice that destruction was coming.
What type of an explosive would kill every organic in Earth, yet leave infrastructure untouched? In most cases the problem is that the Earth itself protects the life on the opposite side of the explosion.
Note that death has to be instant.
You've made three requests:
I'm pretty certain you can't have all of those without magic
The major problem you have is endolithic organisms, which have been found as deep as 3km down and the only reason we haven't found anything deeper is because looking is extremely difficult and expensive. Most likely you'll find stuff deeper still. Delivering enough energy to sterilise rock at that depth without blasting the surface of the planet off is basically impractical, even if you did have a way to attack from all directions at once.
If you're prepared to use handwavium-levels of power and technology, then you could almost imagine some kind of weapon system that could precisely fire perfectly synchronized pulses of some kind of particle and antiparticle that only interacted weakly with normal matter. Once upon a time, Weakly Interacting Massive Particles were a dark matter candidate and something predicted by supersymmetry, but alas no-one ever found a suitable WIMP and SuSy seems to be DOA.
Lets imagine you did manage to create such a thing. Instead of exploding like a bomb, you use massive handwavium particle cannon (which cannot use electromagnetic acceleration!) to produce these perfectly synchronized pulses of WIMPs and anti-WIMPs, shooting them out at high relativistic speeds. Crucially, the first pulse travels ever so slightly slower than the second pulse of antiparticles. As they don't interact via the strong or electromagnetic forces, most of the particles will shoot clean through the Earth, barely noticing it. When they reach the far side, the faster antiparticle burst catches up with the slower particle burst and the two annihilate in a big flash of gamma rays and maybe other exotic radiation.
Fire off as many pulses as deemed necessary, at just the right angles and speeds and intervals such that the whole surface of the Earth and a sufficient amount of the deep crust is simultaneously bathed in deadly radiation that seemingly materializes from nowhere.
Doesn't strike at lightspeed, but may 99% of C is good enough. Given the unwillingness of the particles to interact, such an attack is likely to be highly inefficient and also require exceptionally high levels of technological capability. Just wasting a planet with a shower of antimatter or a relativistic strike would be much more straightforward.
Note: The original idea for this was on the Orion's Arm worldbuilding project, and called "Ghostlight". The page has since been memoryholed, presumably due to project-internal discussions and retconning of things not deemed to be strong enough scifi. No cached copies of the page remain that I could find.
I don't know if that is "instant" enough, but massive amount of radiations and/or short lived radioactive isotopes might obliterate large part of earth life forms and contaminate biosphere enough to kill also tardigrades with time. If done carefully it shouldn't damage directly most of of "infrastructure".
Problem with this schema is it doesn't fit the "explosion" (from a single point out) paradigm; it would still work, but some "carrier" is required. A better paradigm here could be an "implosion" model with a large (virtually infinite) number of radiation sources converging down.
The only thing that travels at light speed are photons.
The most likely origin for this event is therefore an antimatter-matter annihilation bomb, which aptly happens to emit gamma rays. If the bomb splits into at least 3 fragments before the explosion, it can flash the entire surface of Earth with gamma rays.
It's very likely however that organisms living in the deep sea or in deep caves will be sheltered by all that water/rock. But if you really want to sterilize a whole planet, you have to throw a big rock at it and melt it.
The only thing that can kill all life on Earth quickly, including organisms shielded by kilometres of water or rock, without also destroying the planet is neutrinos. But they barely interact with anything, including living organisms, so you’ll need something like the energy of a supernova to create enough of them, and even with total conversion of matter, that means around 5% of a solar mass.
Frame Challenge
Anything capable of interstellar travel and planetary sterilization probably has little or no use for our infrastructure.
If for some reason, whatever sent it wants Earth in one piece, expect one or more relativistic projectiles designed to melt the crust would take care of all those pesky life forms no matter how deeply dug in they are. Berserker goal achieved. ☠️🍻☠️
Otherwise, one or more relativistic projectiles designed to break up the planet would make strip mining much simpler. To prevent possible life contamination, melting the crust before shattering the planet would be advisable.
Oumuamua itself may be too small to launch such projectiles, but it could have a larger companion following the same path about 5 years behind it.
There is a terrifying thing in the universe that does nearly exactly what you want. It's called a Gamma Ray Burst. The origin of these is still being researched at the moment. Our best guesses are that they come from supernovae and/or neutron star mergers, but a civilization bomb would be an interesting alternative explanation for sure.
The explosion of such a kind of gamma ray bomb would travel with light speed, and kill life without destroying infrastructure. (Although you probably want to make it a laser for efficiency reasons.) Only the speed is a bit problematic. The effect of large amounts of gamma rays hitting earth would be the stripping off the ozone layer and the irradiation of the atmosphere as well as all living beings. While the death itself will take some time to set in, it is still instant in the sense that you are completely fucked the instant the radiation his you.
