Luke Skywalker was the real villain
The arch villain of the Star Wars series, Darth Vader, has been grossly misrepresented by historians. In fact he is a Richard III-like character given gross deformities and credited with all sorts of evil deeds to make the story of a supposedly fun rebellion against allegedly harsh overlords seem better, as well as ensure that the writers stayed out of the hands of the dreaded Skywalkerian secret police. Arguing by analogy from earth's history it can be shown that Vader was ordered to eliminate the Jedis as they had become a major obstacle to reform of the military. The famous declaration by Vader that he was Skywalker's son also probably owes much to writers shifting events around for dramatic effect as often happens in films. In fact Luke probably declared himself to be the general's son, long after Vader had been killed in his Death Star.
Mining companies can be good guys.
Academics have gone to so much trouble to whitewash the behavior of the Na'vi, with the 2009 film depicting their side of the story. But the real problem was that the human miners would not agree to hand over their own people to be sacrificed.
Lord of the Rings
Sauron just wanted his ring back
Okay, Sauron was a villain rather than a good guy but Bilbo was still a thief who made the big score - a very valuable ring - and was foolish enough to try bargaining with Sauron over its return, with predictable consequences.
Wayland-Yutani: good reason for denials
The Aliens in the long-running series of films are certainly not good guys but Wayland-Yutani, the corporation supposedly behind the nefarious doings in the first film, were certainly not guilty of all the wild accusations flung at it by the sole survivor of the original expedition.