The overall quest arcs for the Imperial Legion and Stormcloaks are similar, and allow you to unlock the same achievements. Either choice allows you to start a series of quests, during which various battles of the Civil War are fought, ultimately resulting in your chosen side taking control of Skyrim. You will be asked to take sides in the Civil War being fought between the Imperial Legion and the Stormcloaks (a historical description of which may be found here).
