Star trek had plenty of "godlike" characters running through their history...
Of course if you mean just the star trek universe then creatures like the Borg or that other bio adaptive race that defeated the Borg could pose a real threat... Also in star trek tng time travel was accomplished by the Borg....
I. The newest movie time travel resulted and changed the course of history ...
Personally I'm just imaginig a Borg sphere or borg cube asskmilating the deathstsr...
In star trek depending on which show...
In the original you godlike beings thatbpresided over planets. In tng a godlike being shunted the starship around for disobeying him
The q continuum had the ability to alter time/reality as a race and sai eventually in the far further the human race would surpass them so yet were studying the humans before we evolved...
The travelers weren't that powerful at all other than their ability to travel across time and space...
The Borg had shields that could adapt to the energy types ired atnit until they became immune...basically a race of deathlike running around with mini forcefields
They could travel by the voyager series to warp 13 or 13 times the speed of light...by ship and still ha found (atleast the Borg did) means to bridge the universe to cross the entire universe ithrough constructed wormholes...
They had a race of telepaths but they weren't exceptionally powerful... Or at least the halfbreed on the next generation wasn't..
It was shown in the next generation that all races, human Vulcan roman Klingon had similar body types since the original race seeded the rest of the universe with their DNA before dying out...
There are several opponents the star trek people faced that had control over elemental forces controlling planetary wvents like earthquakes storms etc...