Honestly, considering how resilient life is, this would be really, really hard.
Especially as a natural event; most things that immediately spring to mind are either slow enough that life will probably adapt or so devastating that the planet won't recover for millions of years or longer.
There is one thing that might be considered devestating enough to clean a planet of life, without permanently destroying it or the enviroment of the planet.
The passing of a nearby Rogue star. These stars are not bound to a galaxy, but move freely through space. They are very fast, very hot, and sweep throughout the universe. If one of them were to pass near a solar system, it would severely (but very temporarily) destabilize the orbits of its planets, mess with gravity (probably causing intense earthquakes, tsunamis and other natural disasters), suddenly expose the planet to an incredible overdose of solar energy (which might cook alive everything on the surface) and have any number of other of terrifying effects on the planet depending on the kind of star.
But ultimatly, unless the star were to pass so close that it drags the planet entirely out of orbit, it would return to its regular orbit and the effects of the star's passing will be restored.
I'm not sure if this would wipe out all life, but it would certainly clean the surface and might have enough of an effect on the atmosphere that it makes the rest of the planet uninhabitable long enough to deal with whatever still survives underground.
(Especially bacteria and virusses will be a bitch to deal with, those things are really hard to get rid of)