there was a temporal cold war that was the backdrop for the whole series. it was an interesting storyline that spanned most of the run. all of the time travel related to that. the Enterprise crew was a pawn.
there was also a later storyline about the Xindi which paralleled the events of 9/11. they were manipulated into attacking Earth by one of the factions in the temporal cold war IIRC. they were basically told they had to stop earthlings from traveling the stars because in the future, earthlings would destroy them.
the end of the show was a big letdown for many, but once it hit its stride after the first season or two, it was interesting. worth checking out again. i think it was cancelled prematurely due to Star Trek over saturation.
http://www.startrek.com/article/poll-reveals-changed-perception-of-enterprise
Not being able to give it my full attention likely resulted in perhaps a couple of missed episodes, and admittedly I am not a fan of time travel to (IMHO) introduce overly complicated story arcs and timelines (not to be punny!). That said I do recall a few episodes where even though I was unclear as to what was going on they were, in and of themselves, very well done. I was already a big fan of his from Quantum Leap. Producers and networks seem to give up on shows very easily, sadly. ST TNG first season was deplorable, but it eventually got pretty good, and many episodes were exemplary. My new favorite show (Grimm) is likely heading for cancellation after the upcoming (short) season. I doubt I will be as lucky to see it picked up elsewhere as was, for instance, Longmire.