Daniel wakes up injured: it appears that SG-1's appearance on the planet he's on sparked a full scale world war.
In the resulting chaos, a religious zealot manages to gain control, 'purging' those that do not believe in the ancient Gods - obviously the Goa'uld.
With daniel being cut off from the Stargate - and therefore Earth - he hides out with the local resistance. Eventually he's able to get a signal through to the SGC and together they overthrow the new 'government'.
The episode is interesting and well played out, although I think they went a little overboard on the allusions in this one.