Context: There is civilization of God Seekers. They try to prove the existence of (a) God(s) by finding a god-chosen civilization that would be able to survive the genocidal attacks of the God Seekers. The God Seekers are so much more powerful than any other civilization they've encountered, that if a civilization survived despite their best attempts to destroy it, then the most likely explanation is a divine intervention (AKA the civilization was truly chosen by God, AKA a miracle happened).
They’ve already killed everyone else
Your race has already suffered through millennia of the most horrific war imaginable. Their foes could deploy weapons that would sterilise whole clusters of stars. They could deploy defences that would prevent this. Industry, medicine, power generation, basically every aspect of society required to kill and not be killed was elevated to the point of near-magic.
And slowly they whittled down the list of threats. With each enemy defeated they gained experience and tools dedicated to the pursuit of annihilating others. Every star claimed from their foes could be turned to the industry of war. Peace forgotten or, at the very least, viewed as nothing more than a temporary state of affairs.
Until the day they won. All threats comparable to them wiped from existence, your God Seekers were left with arsenals if unimaginably powerful weapons and unfathomable defensive tools, and not one race that could possibly hope to stand against their (now ludicrously over-the-top) military complex.
Oh, and they were left with a warrior race with no enemies, a surefire way for civil war to break out and restart the aeons of bloodshed.
So they let lesser races evolve. They destroy them. Rinse and repeat under the ideology of searching for God.
It isn’t searching for god. It’s a means of exerting political control over a race of hopelessly warlike and aggressive individuals who all have access to planet killing military technology.
But it’s better than the alternative.
The 'how' question can be answered with a technological singularity through artificial intelligence. Due to sheer luck your God Seekers where the first civilization to build an artificial intelligence strong enough to be able to improve itself. Boom, singularity. Only seconds after it was created, it was on a technology level far beyond anything else existing in the galaxy.
The god seekers (or the AI) now know that the only way someone could compete with them is by building a sufficiently powerful AI themself. So they travel through the galaxy and try to kill off anyone who looks like they might be anywhere close. As they are technologically much further advanced than anyone else, they succeed unless there is 'godly intervention'.
An analogy would be that there is only one intelligent species on earth which went from primitive hunter gatherers to space faring in 10.000 years. Any other species evolving similar intelligence would take millions of years. So we would be aware of it and can decide whether we will allow it, boost it or prevent it. The chimps or dolphins or whatever can't really do anything about us.
This civilization unlocked the secret of time-travel. More so, they can detect other civilizations trying to fight them using time travel and prevent it.
God Seekers is a really peaceful civilization. They abhor violence and war. When any other civilization threatens them, they simply travel back in time and make sure that those hostile species would never develop.
However, the ability to time travel is not enough to outclass any other civilization. Normally, what one can do well, the other can do better. Fortunately, all of our universe originate at a single point of Big Bang. Hence, the one who controls the Big Bang, controls the fate of entire universe. God Seekers were fortunate enough to establish a foothold at Big Bang. So far, they had easily thwarted any attempt to unseat them from there. Without control of Big Bang, any attempt to fight them is futile.
If we assume something of exponential grow of civilization, you would reach point when you can literally spam with weapons capable of destroying whole galaxies or more.
If you want know which weapons would do it, list would be quite long, for examples:
- shooting black holes with relativistic speeds onto planets
- forcing stars to go supernova
- directing gamma bursts onto planets
- masses of berserker type von Neumman probes
and many more. Basically any weapon capable of destroying whole planets.
Because someone has to be the best. The universe is infinite, but there are a countable number of spacefaring civilizations. The God-Seekers just happen to be the most advanced, most capable race which has ever graced the universe.
There doesn't have to be a how. How is Michael Phelps the most gifted swimmer in the world? Because someone has to be the best.
Could an opponent potentially arise who could give them a run for their money? Maybe. But their genocidal practices make it fairly likely that any such race is going to get reduced to a scattering of interstellar dust before they reach that point.