Soooo... the thing about Civil War is that it doesn't necessarily make a whole lot of sense. Here it is explained by me though - this will likely be a loooong post.
First off, the 616 universe does not work like our world. Vigilantes are basically never arrested or jailed. The cops most often look the other way, even towards ones like Punisher who kill people, because... well a super-powered villain is not usually something a regular beat cop is gonna be able to handle, basically. Also, the vigilantes are not the only ones with secret identities - by the time Civil War rolls around, there are a few Avengers being sanctioned by higher authorities whose identities are unknown including Spider-Man.
It starts with Tony realizing that there is growing public sentiment against superheroes. People are starting to get bored of having them around and actually be bothered by them - they don't have a lot of accountability, there's not transparency with them and in the case of the ones whose identities are secret there's no way to, for example, hold them responsible or sue them for damages if they're causing problems. The public also starts to get annoyed that supervillains increasingly can't be held in prisons, the heroes refuse to kill them, and often the supervillains only exist and cause mayhem because of a beef with a hero to begin with. So things are tense.
In response to this, Tony and a secret cabal of higher-up heroes who don't normally work together (Reed Richards, Dr. Strange, Professor X, Black Bolt and Black Panther) all agree that actions need to be taken behind the scenes. They start working with the government to ensure that any legislation winds up in their favour and protects the community, and also jettison the Hulk into space. Because he basically represents everything the public hates about the heroes and they know they can't contain him.
Then, a group of young superheroes filming a reality TV show called The New Warriors stupidly chase a supervillain they think they can take into a school zone. It turns out the supervillain is super-juiced up on a new Mutant Growth Hormone that's emerging, and he explodes himself, taking almost all of the New Warriors except one member AND approximately 700 or so schoolchildren with him.
Tinder meet match, basically.
Tony has no choice but to immediately put the best possible government plan into action to register all heroes and disallow secret identities. The difference being that now, not only will vigilantes or local heroes potentially be arrested because law enforcement will be a must, there will also be government teams specifically put together to arrest and capture non-registered heroes.
Tony does this because he knows from his government contacts that the plans prior to his group's negotiations were very extreme - banning certain technologies altogether, chipping and tracking heroes, de-powering them or imprisoning them, etc. So to him registration is the best option and if they don't all go along with it, worse things are inevitable.
Steve, having not been let in on Tony's secret group or knowing this and not probably being willing to go along with it anyway which is why they didn't invite him, basically says "fuck you" to the government when they ask him to work with them to get heroes registered. He teams up with a bunch of the street heroes and heroes who object to go underground and fight the law.
So you then have a situation where Tony is backed into more and more of a corner by public sentiment calling for hero's heads and government legislation to be tougher and tougher, eventually building armor for the government and imprisoning his own friends who he can't make understand that he's trying to help them. And Steve can't back down either because registration represents everything he's against as a strong libertarian who believes that you shouldn't disincentivize people from doing the right thing and helping people if you can.
They nearly kill each other. Tony kind of wins, but then it's revealed that the Skrulls were secretly manipulating the whole thing the whole time and everyone in the 616 pretty much forgets any of it ever happened. (In fact, Tony gets his mind straight-up wiped so he literally forgets it all). The end?
It could have potentially been a really great "Who watches the Watchmen?" type of thing. Instead it was super-angsty whump if you're into that kind of thing and kind of a mess after the fact.
Re: Civil War Query?
First off, the 616 universe does not work like our world. Vigilantes are basically never arrested or jailed. The cops most often look the other way, even towards ones like Punisher who kill people, because... well a super-powered villain is not usually something a regular beat cop is gonna be able to handle, basically. Also, the vigilantes are not the only ones with secret identities - by the time Civil War rolls around, there are a few Avengers being sanctioned by higher authorities whose identities are unknown including Spider-Man.
It starts with Tony realizing that there is growing public sentiment against superheroes. People are starting to get bored of having them around and actually be bothered by them - they don't have a lot of accountability, there's not transparency with them and in the case of the ones whose identities are secret there's no way to, for example, hold them responsible or sue them for damages if they're causing problems. The public also starts to get annoyed that supervillains increasingly can't be held in prisons, the heroes refuse to kill them, and often the supervillains only exist and cause mayhem because of a beef with a hero to begin with. So things are tense.
In response to this, Tony and a secret cabal of higher-up heroes who don't normally work together (Reed Richards, Dr. Strange, Professor X, Black Bolt and Black Panther) all agree that actions need to be taken behind the scenes. They start working with the government to ensure that any legislation winds up in their favour and protects the community, and also jettison the Hulk into space. Because he basically represents everything the public hates about the heroes and they know they can't contain him.
Then, a group of young superheroes filming a reality TV show called The New Warriors stupidly chase a supervillain they think they can take into a school zone. It turns out the supervillain is super-juiced up on a new Mutant Growth Hormone that's emerging, and he explodes himself, taking almost all of the New Warriors except one member AND approximately 700 or so schoolchildren with him.
Tinder meet match, basically.
Tony has no choice but to immediately put the best possible government plan into action to register all heroes and disallow secret identities. The difference being that now, not only will vigilantes or local heroes potentially be arrested because law enforcement will be a must, there will also be government teams specifically put together to arrest and capture non-registered heroes.
Tony does this because he knows from his government contacts that the plans prior to his group's negotiations were very extreme - banning certain technologies altogether, chipping and tracking heroes, de-powering them or imprisoning them, etc. So to him registration is the best option and if they don't all go along with it, worse things are inevitable.
Steve, having not been let in on Tony's secret group or knowing this and not probably being willing to go along with it anyway which is why they didn't invite him, basically says "fuck you" to the government when they ask him to work with them to get heroes registered. He teams up with a bunch of the street heroes and heroes who object to go underground and fight the law.
So you then have a situation where Tony is backed into more and more of a corner by public sentiment calling for hero's heads and government legislation to be tougher and tougher, eventually building armor for the government and imprisoning his own friends who he can't make understand that he's trying to help them. And Steve can't back down either because registration represents everything he's against as a strong libertarian who believes that you shouldn't disincentivize people from doing the right thing and helping people if you can.
They nearly kill each other. Tony kind of wins, but then it's revealed that the Skrulls were secretly manipulating the whole thing the whole time and everyone in the 616 pretty much forgets any of it ever happened. (In fact, Tony gets his mind straight-up wiped so he literally forgets it all). The end?
It could have potentially been a really great "Who watches the Watchmen?" type of thing. Instead it was super-angsty whump if you're into that kind of thing and kind of a mess after the fact.