At 1:21:01 in the film we see a mild version of "the effect" take place, roughly analogous to a pre-shock before an earthquake. All three of the survivors are thrust into alternate versions of Earth, two with drastically differing gravity and one where gravity seems to distort. None of them can see the others and until the effect passes none of them can interact with each other.
It's therefore likely that each time the effect takes place, an alternate Earth is created. Those who're unprotected (e.g. by being dead at the precise moment the original effect) remain in a stable dimension, presumably unaffected. Those who happen to be dead at the time of the effect are thrust into an increasingly unstable pocket dimension. If they somehow then regain consciousness they will find themselves alone on a "Quiet Earth"
From a "Voice of God" perspective, Writer and Director have both stated that the ending was intended to be ambiguous. In his commentary on the Umbrella Entertainment DVD release, writer/producer Sam Pillsbury states,
"...we all thought it was quite simple; I mean, our intention was
just that, what happened was, he died at the moment of the effect for
a second time and he's now found himself in another world, what the
hell's he gonna do...", he then says, more or less jokingly, that
director Geoff Murphy being 'a Catholic or lapsed Catholic, (it) may
well have been something to do with purgatory, and y'know, you being
trapped in cyclical and going back into having to relive your thing
until you work out your karma, (something; possibly 'if I'm not')
mixing my metaphors; anyway, enigmatic is good, I think, to a certain