The Clone Wars era, from 22 BBY to 19 BBY, is a period in time in which the Galactic Republic and the CIS were at war. The war finally ended when Emperor Palpatine had all of the Jedi executed, and the droid army was deactivated.
Certain maps only have the Clone Wars era available, while others have both the Clone Wars and the Galactic Civil War. If the current level is a Clone Wars game, you will only be allowed to side with either the Republic or the CIS. The only exception to this is Assault on Mos Eisley. The Clone Wars takes place during the Rise of The Empire Era that takes place between - but also include the Battle of Geonosis and Battle over Coruscant - Episode 2 and 3.