The Civil War in Skyrim, between the Empire and the Stormcloaks, is one of those rather split stories. Players tend to go one way or the other and stick to their beliefs. It’s really not a clear cut thing like killing or sparing Paarthurnax. Really, the Civil War is a hugely complex issue and one single article can’t really do it justice, but I’ll try.
First off, some specifics. Whatever side you pick in the Civil War, nothing really changes apart from the guards and the Jarls, and a handful of more extreme supporters on either side. Whiterun never gets repaired after its battle, which is very annoying. For you, the player in the game right now, nothing happens. The Thalmor are still present. There’s still camps of whoever lost the war hanging around in the wilderness. Dragons will still attack you. Your consequences have no major effect on the world, yet the Civil War can’t be completed without you.
It is clear though that from the start, the game WANTS you to side with the Stormcloaks. The Stormcloaks with their cooler names and fluffy armour have clearly been captured and treated as pesky rebels that need to be killed. And you run off with a bunch of Stormcloaks into that tower when Alduin first attacks. After all, the Imperials were about to chop your head off without letting you have a trial or anything. The Imperials are clearly evil, right?
Look at it another way though. The Imperials just captured a bunch of men and women who had been terrorizing the Imperial areas of Skyrim and they caught you too. What were you doing so close to those Stormcloaks? It’s very easy for the Imperials to think that you too are a Stormcloak. That is no excuse for not letting you have a trial, but when you’re dealing with someone who shouted the previous High King of Skyrim to death then declared war on the empire who hadn’t done that much wrong, I can see why they want to stamp out this threat before it gets worse. We’re at war, after all.
Once you’ve escaped Helgen, you’re given an option to join up with the army of whoever you escaped with. Luckily, no matter what they say, you’re free to choose either the Imperials or the Stormcloaks, or never choose at all. There’s also a chance to change your mind when you set off to find the Jagged Crown, you can betray your current side and join the enemy.
But why are both sides fighting? The Stormcloaks want to succeed from the Empire and gain independence because they believe that the Empire is weak and gave in to the Thalmor. The Empire doesn’t want to be split up and really, they hate the Thalmor as well. The main thing the Stormcloaks want more than anything else is to be able to worship Talos as much as they want. Currently, the Imperials can’t allow the open worship of Talos to keep the Thalmor happy, so the Stormcloaks seem somewhat justified in their rebellion.
The crucial information here though isn’t really obvious.
Before the Stormcloaks appeared, Talos worship was forbidden, but it was like marijuana in the UK, no one in Skyrim was ever arrested for worshiping Talos and no one enforced the law. As you walk through Whiterun, you can see this, there’s a loud-mouthed priest of Talos shouting in the main square in front of the Companions’ HQ. There are statues of Talos everywhere. And people are still allowed to wear their amulets. It wasn’t until Ulfric made a huge fuss that the Thalmor caught wind of all this heresy in Skyrim, and forced the Empire to let the Thalmor set up camp there and start prosecuting people.
Of course, Ulfric has been working for the Thalmor (unknowingly or not, we don’t know) for a long time. He may have tried to sever contact with them, but he’s a Thalmor asset. The player finds this out, it’s written, by a Thalmor boss, in a document you can steal in Diplomatic Immunity.
And if Skyrim gains independence, they isolate themselves. You could suggest that Skyrim makes an alliance with Hammerfell, especially when Hammerfell managed to fend off the invaders, but it doesn’t always work like that. I doubt the somewhat xenophobic Nords would work well with the also somewhat xenophobic Redguards. Plus, the only reason why Hammerfell did alright is the same reason no one really manages to invade Russia – it’s a horrible, harsh environment that most invaders underestimate. I doubt they’ll leave the safety of Hammerfell to defend some stupid cold land up north.
Whether you believe that to still be true, or you think Ulfric is free from their influence, or Skyrim will be fine on their own, it doesn’t really matter. The Thalmor want the Civil War to go on for as long as possible, because the longer men fight with each other, the more time the Thalmor have to rebuild their own armies. Elves don’t reproduce as fast as men, and this is a huge opportunity for them. And if the Civil War ends, after years of fighting? The Thalmor can just stomp all over everyone.
What people forget is that Thalmor don’t want to conquer everyone. They want to destroy everyone. Their end-game isn’t world domination or anything like that, they literally want to end existence, because that is how they believe they will become eternal spirits again. If the Nords can beat the Thalmor, fine, but what if they can’t? It’s a huge risk to take, especially when the entirety of the universe is at stake.
That’s not to say that Skyrim shouldn’t have independence. Every nation should have that right. The problem right now is that the Stormcloaks picked the worst time for their rebellion. During a time of peace where men should have been resting, repairing and repopulating for a second war against the Thalmor, Ulfric has decided that now is the best time to start making a noise. It turns out that Ulfric is helping the Thalmor, whether he knows it or not.
Whoever wins after the Civil War, everyone is weak. Apart from the Thalmor.
The best course of action is so simple. End the Civil War as fast as possible in favor of the Empire, destroy the Thalmor, THEN free Skyrim.