I want to say it was called something like 'Time Storm', but I haven't had any luck locating it.
The main character was (I believe) caught up in some form of storm that somehow unseated him from time, and dropped him into some structure (I believe it had non-euclidian geometry connecting the rooms) where a number of beings used some method to project their conciousness back in time to influence various historical beings. This influence seems to be very negative, as they seem to be stoking the fires of Man's worse traits, making him more violent and so forth.
Our hero finds some way to attack them, end eliminate them from the structure, then sets about on a long chore of changing things back and making man a 'better being.' After quite a while, he has accomplished his chore (this location being outside of time, I don't think he ages) and ends up re-inserting himself into time.
Only to witness mankind being attacked and subjugated by aliens (possibly from outside of his time or something) now that man is harmless.
The twist at the feels kind of like Fredric Brown, but I haven't had any luck finding it. Any ideas?