Scale down the typical Big Threat to a more reasonable level, and treat the apocalyptic bad guy as the once-in-ten-thousand-years type of event it semi-realistically should be? Which incidentally means having an apocalyptic threat no more than once in the series, ever, and making a giant season-spanning myth arc, if not a multi-season long one, to build up to it.

Babylon 5 did a good job of it with the Shadow War.