Skyrim's Civil War is the second questline most central to the game's main story, next only to the main quest itself. The province's Civil War is the final prophesized event before the return of the dragons, and the game famously opens with the disruption of Ulfric Stormcloak's execution when Alduin the World Eater returns to Tamriel.
There's one main quest which is rendered completely unnecessary if the player has completed Skyrim's Civil War questline, because the quest itself revolves around brokering a brief peace between the warring factions. However, there are many more instances where the outcome of the Civil War can affect Skyrim's main quest.
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The outcome of Skyrim's Civil War questline most notably effects the main quest "Seasons Unending." This quest begins after the Dragonborn fails to kill Alduin at the Throat of the World, and has to formulate a new plan. The player must go to Whiterun in order to convince the Jarl to help them trap a dragon. However, if the Civil War questline has not been completed the Jarl will refuse to help unless there is a reprise in the fighting between the Imperial Legion and the Stormcloaks.
For obvious reasons this quest is not triggered if the player has also delivered a decisive victory for one side or another. If the players sided with the Imperials Jarl Balgruuf will agree to help, while if they sided with the Stormcloaks the new Jarl, Vignar Gray-Mane, will also be quick to agree. There is no need to get the Greymanes involved as peacemakers, and there is no opportunity to get involved in Ulfric, Tulius, and Thalmor Ambassador Elenwen arguing the terms of the treaty.
This is not the only main quest that is changed by the player completing the Civil War questline, however. During the quest "Sovngarde" where the player enters the Nordic afterlife, they can find some of the characters from both sides of the Civil War that they killed, depending on which side they chose.
If the players have killed Ulfric Stormcloak they'll find the once proud Jarl of Windhelm lost in the mists, where Alduin is devouring the souls of dead Nords trying to make it to the Hall of Valor. Ulfric reflects upon the war: "Skyrim was betrayed, the blood of her sons killed in a doomed struggle against fate. And so in death, too late, I learn the truth - fed by war, so waxed the power of Alduin, World-Eater - wisdom now useless. By gods' jest in this grim mist together snared, Stormcloak and Imperial, we wander hopeless, waiting for succor. Turn back before he finds you. There is no escape, courage is useless."
It's a poignant reflection on his life from a man more prone to using his voice for combat than poetry, and an interesting and somewhat sympathetic end to Ulfric's arc for any player who sided with the Empire of Tamriel. Ulfric's second, Galmar Stone-first, can also be found in the fog, and is far less forgiving. "Dragonborn, even in death you dog my steps?" he asks, before adding, "how come you're here? The king of this realm will cast you out - cursed be your name by all sons of Skyrim, with scorn unceasing."
This segment ultimately proves more dialogue for players who sided with the Imperials, but for those who sided with the Stormcloaks they can find Legate Rikke lost in the fog. She'll reflect that "the bitter war in the world beyond was all for naught" and says she is "weary and lost." As an Imperial, General Tulius' soul is nowhere to be found, escaping the fate of the souls lost in a war he helped sustain. His absence may not lead to memorable lines like Ulfric's, but it is an interesting reflection on his detached role as an Imperial governor to begin with.
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The Civil War isn't just interesting because of the changes it makes to Skyrim's main quest, but also some of the things that stay the same. A huge part of the Stormcloaks' motivation for removing the Empire from Skyrim involves the Thalmor. At the end of the Great War between the Empire and the Aldmeri Dominion, the two sides signed the White-Gold Concordat. Part of this treaty allowed the Thalmor to roam freely throughout the Imperial provinces persecuting Talos worshippers due to their belief that no human could have ascended to godhood.
However, if the player sides with the Stormcloaks during the Civil War, there are two quests where the Thalmor presence is still felt. During the quest "Diplomatic Immunity", the player will still be sent to the Thalmor Embassy, showing that the Aldmeri Dominion still has a presence in Skyrim. This suggests that as an independent nation, Skyrim may have jumped from the frying pan into the fire, still forced to abide the presence of the far stronger Dominion even if the High Elves are no longer able to legally police Talos worship.
The Thalmor are also seen to retain spies throughout Skyrim. In the quest "A Cornered Rat" players have to find Esbern in the Ratway in Riften before the Thalmor do. This is also unaffected by a Stormcloak victory, and the fact that the Thalmor are still able to operate in the underbelly of one of Skyrim's hold capitals should be cause for concern for any player who dislikes the Dominion.
The effects of the Civil War on the main questline have sobering implications for the Stormcloaks no matter which side the player chooses. If they side with Ulfric, they'll find that he remains unable to prevent the Thalmor from operating within his borders, just as the Imperials were. If they side with the Empire, they'll find Ulfric in Sovngarde lamented the blood spilled by the war he helped start, and implying that he may have made other decisions had he been a wiser man. It's an interesting detail for Bethesda to include, and one which adds a more complicated tone to the sympathetic light the Stormcloaks are cast in during the game's introduction.
Skyrim is available to play now on PC, PlayStation 4, PlayStation 5, Xbox One, Xbox Series X, and Nintendo Switch.