The Skyrim Civil War (called the Stormcloak Rebellion by the Empire and the Great Uprising by the Stormcloaks) is an ongoing civil war in the province of Skyrim. It began when High King Torygg was slain by the Jarl of Windhelm, Ulfric Stormcloak, who then initiated the Stormcloak Rebellion.  
The Stormcloaks believe that the Empire betrayed Skyrim by signing the White-Gold Concordat with the Aldmeri Dominion at the end of the Great War. The Concordat binds the Empire to several Thalmor demands, including the outlawing of Talos worship, and the Stormcloaks feel that the Thalmor have far too much influence over the Empire. The Imperial Legion see the Stormcloaks as traitors — partly due to their desire to secede from the Empire and partly because of Ulfric's killing of High King Torygg — and seek to crush the rebellion and prevent it from taking control of Skyrim.
The Stormcloak uprising was founded by Jarl Ulfric Stormcloak of Eastmarch after the Markarth Incident, and aims to remove the Imperial Legion from Skyrim's territories and turn the province into an independent kingdom. The rebels' stated goals include lifting the ban on Talos worship across Skyrim, expelling or executing all the Thalmor Justiciars who have been granted the authority by the Empire to enforce the White-Gold Concordat within the province, and to independently prepare Skyrim for a future war with the Aldmeri Dominion. Besides stemming from deep discontentment with the ban on Talos worship among much of the Nord population, a secondary motivation behind the Stormcloak uprising is the belief that the Mede Empire has become a puppet state of the Thalmor in all but name, and no longer has the legitimacy to rule over Skyrim.
The Stormcloak rebellion represents a large enough portion of Skyrim's population to have triggered civil wars. Some Nords, notably Jarl Laila Law-Giver of Riften, do not entirely trust or support Ulfric himself but back the Stormcloaks as they share the common goal of independence from the Empire, while others feel the civil war bleeds Skyrim dry and will leave the Thalmor as the sole beneficiaries. After the White-Gold Concordat was ratified and the worship of Talos became outlawed, some of Skyrim's populace began to view Imperial rule as the illegal occupation of their lands, and many Nord men and women would volunteer to take up arms against the Empire under the banner of Ulfric Stormcloak while other Nords choose to join the Imperial Legion.
The name "Stormcloaks" was invented by the Empire in an attempt to belittle the uprising, by implying that its supporters are Ulfric's personal lackeys in his bid for power. They have since defiantly taken the name and made it their own, to honor the common cause of Skyrim's independence they are fighting for.
The Imperial Legion is the military arm of the Empire, which prior to its Great War with the Aldmeri Dominion ruled over most of Tamriel. The Legion is attempting to quell the rebellion led by Ulfric Stormcloak, with the goal of keeping Skyrim in the Empire and strictly enforcing the terms of the White-Gold Concordat within the province.
Several of Skyrim's more affluent Jarls and citizens are still supportive of the Legion, as they feel Ulfric's speeches amount to political posturing and that his underlying motive is to become Skyrim's new High King.
The Dragonborn sometimes will encounter a Redguard citizen on the roads who is heading to Windhelm to join the Stormcloak uprising, stating that "the Empire is in shambles" and that "Ulfric has the right of it". Similarly, they can also encounter a Dunmer citizen heading to Solitude, stating that "A united Empire is best for everyone" and "I was born and raised in Skyrim, but the Nords treat us like dirt".
General Tullius is the military governor of Skyrim and the commander of the Legion in the province. He and Jarl Elisif of Haafingar lead the Imperial war effort. In Skyrim, the Legion is headquartered at Castle Dour in the city of Solitude, with Legate Rikke serving as their field commander.
Initially, both the Empire and the Stormcloak Rebellion control four Holds. The Empire controls Falkreath, Haafingar, Hjaalmarch, and the Reach, while the Stormcloaks control Eastmarch, the Pale, the Rift and Winterhold. Balgruuf the Greater, Jarl of the central Whiterun Hold, remains uneasily neutral, but he will eventually side with the Empire once the war is joined, regardless of which side the Dragonborn chooses.
- Depending on the order in which they are completed, the Civil War can have an impact on the Main Quest, and vice versa. In the main quest, Season Unending is a meeting between five factions (the Stormcloaks, the Legion, the Blades, the Thalmor and the Greybeards) to negotiate a truce, which temporarily pauses the Civil War.
- If the Civil War is completed before Season Unending, the peace conference will not be held, and the later quest will not occur.
- If Season Unending is completed before the Civil War ends, it will change territories under the control of both the Imperials and the Stormcloaks.
- A bounty may be cleared when the relevant Hold is liberated or reunified during the Civil War.
- When the Thalmor Dossier on Ulfric Stormcloak is found, it states that if either side wins the Civil War it would negatively affect the Thalmor's goals, they claim that an ideal situation would be a long war in which neither side truly "wins".
- Even though they play a major part in the tension between the Stormcloaks and the Imperial Legion, the Thalmor play no major part in the war.
- In The Elder Scrolls V: Dawnguard quest Awakening, the Dragonborn may ask the vampire Serana how long she's been sealed in Dimhollow Crypt. As she will have no idea, she will ask "Who is Skyrim's High King?" after. By this point, the Dragonborn can refer to the Civil War as "a matter of debate" or voice their support for either Ulfric Stormcloak or Elisif the Fair. Obviously, she will not recognize either Jarl due to the amount of time she's been sealed, hiding from her father under her mother's instruction.