In the last few episodes I've seen travel into the past to stop an alien plot (see also DS9 in the 60's and TNG in 1849). There was an alternate future that undid itself by the end of the episode (see also innumerable episodes of TNG), and a few others. Now we're back to social commentary: a group of religious zealots intent on eliminating the heretics on their homeworld ("they think the world took one day longer to create than we do") sieze control of Enterprise by setting up a group of suicide bombers around the ship. Meanwhile, Phlox and Archer learn of dissent in the ranks when one of the women in the group wants to have a space abortion.
I'm always amused by the Trek representation of religion. All alien religion is either insane and dangerous or hilarious, with the exception of Bajoran religion as practised by Kira or that hot priest, but not by anybody else. Sisko's involvement is OK, since he maintains that the Prophets are The Wormhole Aliens. (Idea for a novelty album: Gul Dukat and the Wormhole Aliens.) Also tolerable is Vulcan religion, since it's just like Zen (as depicted in pop culture). Meanwhile, there is no human religion, as far as we can tell. When humans talk about how they finally overcame war, poverty, and prejudice, they never include religion in that list. Then again, we never hear about anyone having any sort of belief in anything.
I'd love to see an episode in which a character casually mentions the dissolution of the Apostolic See in late 2082. Even better would be a crewman consulting the computer-run holographic Chaplain. Maybe they could get Dean Stockwell to guest star.