Relativistic missiles. Nothing moves faster than the speed of light. So if you can get a big rock to go 95% of the speed of light, we'd only be able to detect that it's coming right as it hits.
This is a very common answer to "how", but it comes with lots of problems in the Dark Forest context.
If you actually calculate how much energy is required to boost a big rock up to that speed you run into lots of difficulties. It takes a lot, a heck of a lot. How does a civilization that is "hiding" accumulate that energy? How does it store it long-term?
How is that energy actually put into the rock? This is basically a starship accelerating up to that speed and getting a starship up to that velocity is not easy even if you have the energy available. Does it have a rocket? The rocket equation for getting up to near-lightspeed requires ridiculous amounts of propellant. Is it beam-propelled? You're not being at all stealthy that way. How much acceleration can you get out of your system? It takes a full year at one Earth gravity of acceleration to get up near lightspeed, and that's a really high acceleration - you generally trade acceleration for efficiency so the faster you want to get up to speed the more energy you need and the noisier you'll be.
It actually is possible to counter an RKV. It's much easier to hit and destroy an RKV than it is to launch it, all you need to do is get a pebble in its path. The key is detection, and the above points give some pretty good options for detecting it before and during launch. That gives you time to fire your countermeasures.
And ESPECIALLY if your civilization is still mostly planetbound.
Absolutely not guaranteed to be the case. Earth's civilization could have easily had offworld colonies by now if circumstances had been slightly different, so a Fermi paradox solution that requires reliably blowing up Earthlike civilizations before they can get offworld doesn't work. They're already too late.
As I said previously, Earth has been quite obviously life-bearing for at least 2 billion years. Why wait until something like an RKV is needed, and even that is not guaranteed? They could have destroyed life on Earth far easier, and thus far more stealthily, if they'd done it a billion years ago.