In video games, you're usually on the side of good, and you spend all your time fighting evil forces in hopes of stopping their devious plans. But not all games are that simple. The morality of some titles is a bit more complicated.
You can spend a lot of time believing that you are fighting for what is right, only to later discover that you are actually on the side of evil. That doesn't always mean your opposition is pure of heart, but they are often better than those you side with. Here are some examples of that phenomenon.
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In Crackdown, you play as a superpowered agent for a group called the Agency. The organization has been hired to clean up Pacific City, which has been taken over by various gangs. Throughout the game, you systematically get rid of these gangs by eliminating their main members. By the end, the city is almost crime-free.

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Yet that's when you discover that the agency had secretly supplied all the gangs in the first place and orchestrated the whole thing to allow these groups to take over the city. The agency set it up so that the townspeople would need them to come in and take control. Therefore, even though the gangs are not morally good by any standard, you worked for the most evil group of all.
Red Dead Redemption
Right from the start of Red Dead Redemption, you're doing the bidding of some government agents. They have tasked you, John Marston, with eliminating the remaining members of the outlaw gang you used to run with.
Since they've taken your family away from you and forced you to work for them, the agents aren't exactly the good guys in this scenario. But you play as an ex-assassin hunting other assassins, so they seem to be the most morally good side by default. But they really aren't. This is shown at the end when you have done everything they say, and they still come to your home to kill you. At this moment, they show that they are just as bad, if not worse, than your former gang members.
Haze
Haze is a first-person shooter where you play as a soldier for the Mantel Corporation. You're not just a basic soldier either. The Corporation gives you all a supplement called Nectar to enhance your abilities. Now, based on this alone, it's reasonable to assume that you're playing for the bad guys, since it's a company that gives you drugs. Still, the game does a decent job of painting the rebels you fight as the villains, as they wreak havoc in a region of South America.
For most of the mission to eliminate them, it seems fine. However, you slowly learn that the nectar in your body prevents you from seeing reality. That reality is that you are monsters who do terrible things, and the rebels are actually not as bad as they have been made out to be.
Grand Theft Auto 4
During part of GTA 4's main story, you work with Mikhail Faustin and Dimitri Rascalov. Mikhail is a short-tempered man who orders you to kill the son of a powerful Russian mobster. Afterwards, Dimitri comes to you and reveals that the mobster will spare you if you eliminate Faustin.
So, you do, but then Dimitri promptly betrays you by revealing that he's actually working with one of Niko's (protagonist) sworn enemies, Ray Bulgarin. At this point, it's clear that lining up for Dimitri was a mistake. After all, there was no sign that Faustin would betray you, and from Niko's perspective, pretty much nobody is worse than Bulgarin.
Spec Ops: The Line
Spec Ops: The Line lets you lead Delta Squad to Dubai on a reconnaissance mission to see what happened to the 33rd Infantry. They were supposed to evacuate people after a disaster, but they never got out. Once there, you learn that the 33rd has done some morally questionable things during his time in Dubai.
Throughout the game you also do some messed up things as you are tricked by the leader of the 33rd, Konrad. By the time you meet him, however, he's already dead and has been since before you arrived in Dubai. It turns out you've been hallucinating events, and most of the horrible things that happened during the game were because of you, not the 33rd.
Ratchet And Clank: Going Commando
At the beginning of Ratchet and Clank: Going Commando, you are hired by MegaCorp to track down a thief who has stolen an unusual creature created by the company. Eventually you manage to get the experiment away from her and hand it over to your MegaCorp boss. It seems like a job well done. But then the thief tracks you down and reveals that she is a former MegaCorp scientist.
The experiment she stole is a threat to the entire galaxy, as it has a habit of turning violent. She took it from MegaCorp to try and save everyone. Therefore, she is the true hero, and your bosses can stop getting everyone killed thanks to you. Thankfully, that doesn't happen.
Assassin's Creed 3
In the early hours of Assassin's Creed 3, you play as a charming man named Haytham Kenway. As him, you go on various missions where you murder some people who seem to deserve it. Along the way, you recruit a bunch of men and form a small group. Since this is an AC game, assume you're building a small band of Assassins.
That is until Haytham introduces a new member to the crew and names him a Templar, who are the Assassin's main rivals. Then you gain control of Haytham's son, Ratonhnhake:ton. He actually becomes an assassin and spends the rest of the game hunting down all the Templars you were tricked into supporting in the first few hours of the adventure.
Portal 2
In the original Portal game, the main villain is an AI that forces you to complete tests in a science facility before trying to kill you. That AI is GlaDOS, who returns in Portal 2. It's understandable if, after the previous game, you're not a big fan of the machine that tried to burn you alive.
To stop her, you team up with a small bot named Wheatley. But unfortunately, when you remove her from her position in control of the facility, you hand the reins over to Wheatley. This is a problem because he immediately goes mad with power. He prevents you from leaving and forces you to complete the tests that GlaDOS made you do. He is arguably even worse than her.
Early on in Metal Gear Solid 2, the heroes and villains seem clearly defined. After all, terrorists have taken over an offshore facility and captured the President of the United States, while you have been sent there to stop them. However, Metal Gear Solid is never that simple. Deep into the game, you learn that you actually work for the Patriots. They are a secret organization that rules America and controls the population. And they do it in nasty ways.
The entire terrorist attack had been created by the Patriots to test and improve their AI's ability to manipulate events and control people. The main character trying to stop them is the game's main antagonist, Solidus Snake. He's not a good guy by any means, but he's still not as bad as the Patriots.
Far cry 4
Far Cry 4 puts you in the role of Ajay, who travels to Kyrat to fulfill his mother's last wish by returning her ashes to Lakshmana. The situation there is not good, and you end up having to join The Golden Path in an attempt to stop the country's dictator, Pagan Min. Unfortunately, the two leaders of the group, Amita and Sabal, are just as evil as Min.
This will appear if you end up controlling any of them. Both have terrible plans for the population. Pagan Min, on the other hand, wanted to lead you to Laskhmana all along because that's actually the name of he and your mother's deceased daughter. Once you place your mother's ashes next to her daughter, Pagan Min lets you become the new ruler of Kyrat, which is the best outcome for the nation.
