Threads of Time are overall modifiers that are gained through world resets. The amount given depends on how much you have upgraded cities in their skills.
It is not recommended to reset the game excessively, as it will take longer to reacquire the citizens needed to gain further threads of time.
Threads through CitizensEdit
Ignoring all other methods, you get 1 thread for every 200 villagers beyond your previous villager count at last reset.
Example: If you trained 210 Citizens then perform your first reset you'll receive 1 thread. You will then need to train 410 citizens to get a thread on your next reset.
Where is Threads received, is current citizen count, and was the citizen count at the time of last reset.