Pandora. A place where you will not find a more wretched hive of scum and villainy. You must be careful. There are bullymongs (bonerfarts), skaggs, super irritating-flying dinosaur-assholes, robots, bandits, and you. Yes that's right, you are one of the worst things on this planet. There is one shining beacon of hope to finally bring an end to all the sociopathic murder, deceit, greed, violence, ignorance, and pain -- and that's Handsome Jack.
Don't believe me? Think I'm just writing this to present a counter-view to the already established protagonist/antagonist relationship to get some page reads? Maybe, and you'd be correct in the realization that Handsome Jack is, without a doubt, the antagonist of Borderlands 2, but you'd be mistaken to think he is the evil one. Let's take a look.
Why you think Handsome Jack is the Badguy:
Because he's not you. This is a pretty simple statement, and I don't think anyone was confused about what side of the game you're supposed to be playing on/supporting. However, if there is one thing nerd-culture has presented to audiences through shows like Game of Thrones, it's that perspective is a powerful force of interpretation. Who is it that you are interacting with in Borderlands 2 that would ever make you think that you were on the side of "good"? Here's the roster.
This might be one of he tougher ones to see, as Roland is described by everyone as being amazing. He's calm, collected, a seemingly natural leader, and is interested in creating a sanctuary for the oppressed of Pandora in a city called ... Sanctuary. Okay, so he's not very creative, but how can you speak negatively of a guy trying to save others? Simple, you look at who he is trying to save.
Look at the people in Sanctuary. We'll go one by one through this penitentiary of sociopathic psychos just to really nail the issue into your brain. First, you have our favorite doctor from the first game, Zed. Zed is an admitted fraud; proudly pointing out that he doesn't have a degree or license in any medical field whatsoever, and he still asks you to perform duties for him for his purposes of "study." A few examples of his requests involve murdering a man with an Eridium powered gun, then using that rifle to kill bandits in order to study the effects of shooting highly charged projectiles through living flesh. But hey, those are bandits, so who cares about them? He also asks you collect body parts, but in a timely manner so they don't rot away before he can use them. Yeah, you helped in illegal body part trafficking. That's fine though, Pandora is a crazy place and you need to do what you need to do to survive.
Also don't think about how he is knowingly profiting off of your carnage.
Then there is the dishonest, cheating, manipulative weapons dealer, Marcus. If there is one mission that will really point out what a horrible, selfish, and callous individual he is, it is the one in Sawtooth Gap, where you have to find Kai and retrieve nine-dollars. If you listen to the ECHOS you will hear Marcus tricking a poor geek into thinking he is a chosen one in order to sell him some shit equipment, which ends up leading to this person being murdered. What's Marcus' concern? Nine-dollars. He also asks you to go collect refund checks that he should have been issuing anyway from people he admittedly cheated. But you don't think anything of it because of the amount of ridiculousness that is already happening on this planet. Keep that in mind for later, because this is your established perspective.
Then there is the cultured, accented scientist and knighted (we assume) intellectual, Sir Hammerlock.
He comes off as polite, and even lets you into his city at the very beginning of the game. Granted, it's to murder some bandits, but he let you in and reattached Claptrap's eye. So, he's a nice guy, right?
Wrong. This guy screams fraud, and seems to get his jollies off on taking out personal revenge on a tier of the animal kingdom that is responsible for his lost limbs. How little respect does he have for the life on this planet? Well, for starters, he asks you for the hides of some local bullymongs. Not a big deal, as there must clearly be a reason why he can't capture one instead. He also, for some reason, doesn't like the name "bullymong." There must be something aesthetically wrong with that, but that's not your concern because he's dangling a weapon in front of your face as a reward. After renaming them Bonerfarts, then going back to the original name, he asks you to see what grenades do to these lumbering beasts. This is already after you've killed about 20 of them. I'm pretty sure you could guess what happens when a grenade goes off next to something, but there's got to be a good reason for his methods. Surely it will get explained at some point!
Then there is the fanservice that are Moxxi's breasts. A returning character from an expansion of the original Borderlands; Moxxi is well known because she used to run tournaments of death. Think about that. You are helping and assisting a woman who made insane amounts of money off of mass homicide. Which you can apparently do with a throbbing erection, because that cleavage and her promise of gear takes away any thought into the ethics of what you're doing. So, why is she serving in a bar instead of running her games of death? Because Handsome Jack destroyed her arena.
Thankfully, there are two other arenas you can go to in order to massacre large amounts of people for money and weapons. Because, as the "good guy," you need better gear to stop this "evil" individual who is going after the same thing you are.
Let's not forget Scooter. A man so sexually twisted that a poem of his causes a woman to commit suicide, another woman to go isolate herself with a bandit group known as the "rats," and not to mention his own sister caught him with feelings for her at one time (which he doesn't deny). But he lets you move quickly on wheels, so we'll forgive him.
Then there are the vault hunters from the previous game.
Brick is a psychopath who derives pleasure from killing people. He is the leader of the "Slab" bandits, who attack you with the same ferocity and disregard for anything rational as the rest of the baddies on this planet. Brick is their LEADER, and he kills them on a whim and doesn't even feel bad about it. He also killed a man by cracking his skull open like an egg with his thumbs as the man begged for mercy. No wonder Facey McShooty wants you to shoot him in the face when you're in Slab territory. Then there's Lilith, who also happens to be the most powerful Siren on the planet. What's she doing now? She is revered as a Goddess to a local faction of bandits. Yup, another leadership role to a group of murderers and killers. Instead of pointing them in a positive direction she makes them kill each other so Roland can focus on fighting Jack. But, as we've gone over, it doesn't matter to you because you want their stuff, and you find death on Pandora humorous. Mordecai might be the only one out of the group who isn't a serial killer under his mask. Until his bird gets killed, that is.
Perhaps that's what happens when you go vault hunting and discover that what you've really been gun-lusting after is a giant monster the entire time.
Here is why Jack is actually good:
He is trying to use The Warrior for peace. He wants to eliminate the savage monsters, the constant violence from the warring bandit tribes, and destroy Roland and his uprising. It's only the previous vault hunters who make the assumption that Jack is going to destroy the planet.
Jack creates a city -- Opportunity -- that may be a bit fascist, but, on a planet like Pandora, that's probably what is needed to restore some semblance of order to the chaos. He is providing jobs, a safe environment, and is pretty careful about who he will let live there once the construction is complete. If you listen to the recordings over the loud speakers Jack won't even let the engineers live there once construction is done. It will probably be automated, so that when the city begins to flourish it won't be populated with builders who can also be willing to murder a stranger at the drop of a hat.
Then we have Angel, his Siren-daughter. Jack mentions that Angel did something terrible to her mother when she was a child. This is what caused jack to house her in the Eridium pen that you find her in 3/4's of the way through the game. What a cruel bastard! Roland even points out that someone who does this to their daughter doesn't deserve to live.
We've seen what an unchained Siren can do with Lilith. Jack is also using her abilities in order to try and create his version of peace. The password to enter her chambers is "I love you;" something that he programmed himself as a constant reminder of why he is doing what he is doing. At one point, he even tells you to forget about the key to the vault, and realize that it is an innocent human life that you are about to destroy for ... what, exactly? You're doing it for gear. Roland is doing it for Sanctuary, we think. So, you then proceed to kill Jack's daughter, who is obviously mad at her daddy for keeping her locked in her room because of the damage she can create.
And don't think that Jack isn't merciful. He owns the machines that bring you back to life each time, so he obviously is giving you plenty of opportunities to see the error of your ways.
So with all this information, why does he come off as the badguy?
Easy -- he's an asshole. Jack is good at what he does, and he knows it. He believes so highly in himself and what his plans are that he becomes narcissistic, as many uber intelligent people tend to do. Because he says mean things to you he becomes the villain. To be more accurate, your antagonist. Jack isn't the one killing people for relics, elbow spikes, shields, guns, ammo, and some life experience. You ruin everything, Vault Hunter, and you should feel bad for it. Really bad. Until you see what unnamed abilities that orange weapon can do, and need to find a new camp of living organisms to test it out on. However, there is good news. Now that you've stopped Jack you've been able to find other planets with Vaults on them. As Lilith says, in a nice allusion to the marketing music from the first game, "Ain't no rest for the wicked." How true, you sick bastard.