Long before Pokémon X/Y would introduce Malva, the villainous Team Flare member of the Elite Four, the Pokémon Adventures manga had already turned the entire upper echelon of the Pokémon League into full-blown villains. No longer the paragons of virtue unified with strength portrayed in the games, the manga had some fun with the characters and motivations of the original Kanto Elite Four members before allowing future Elite Fours a chance to shine as allies instead of adversaries.
Debuting towards the end of Volume 3 as shadowy figures, the Elite Four would go on to change the world for all the right reasons... but with the wrong methods. Comprised of the vicious dragon master, Lance, the vengeful ghost whisperer, Agatha, the thrill-seeking fighter, Bruno and the icy cutthroat, Lorelei, the four work together to accomplish a surprisingly admirable goal: creating a paradise for Pokémon where they will no longer be hurt by human activities. It's not their goal that makes them evil, it's their methods of getting there -- namely, that they intend to create this paradise by eliminating the human race from the equation altogether.
The four begin to take out key targets, overwhelming Red with an unfair three-on-one battle and starting to target others who could interfere with their plans. Fitting for Adventures characters, they also have some rather unfair abilities giving them the upper hand, such as Lorelei's ice dolls that allow her to freeze opposing trainers and Pokémon, or Lance's abilities to read the minds of Pokémon and heal them.
But even with their abilities, they aren't quite strong enough to overwhelm the Pokédex holders and Gym Leaders together -- and so they hatch a scheme to get all eight badges and amplify their powers to control a giant bird-like Pokémon, heavily implied to be Lugia. While they are, of course, eventually defeated, each one of them is painted as a complex character who is able to keep our heroes on the ropes by their unpredictability and teamwork.
Due to their "noble" goal, they have some superb teamwork and are willing to help both each other and their Pokémon out. Since their Pokémon are not expendable and have been truly cared for, their Pokémon will continue fighting for their cause even without their trainer nearby to give direct orders.
However, on an individual scale, their goals vary ever so slightly. Lance, the ringleader, is the most aligned with the group's overall goals, being able to fully understand the pain that humans have put Pokémon through, he has come to despise his very kind and earnestly seeks their destruction so that Pokémon can thrive. Lorelei is the next closest to this ideal, wanting a refuge for Pokémon where they can live away from humans' toxic byproducts, but not necessarily through the eradication of the human race.
As a result, she tends to act slightly more manipulatively, trying to obtain that which she seeks through the easiest method -- even offering Red a spot on their team, recognizing how valuable of an ally he could be. However, being frozen to her ideals means that she expects others are the same way, and so she only makes the offer once before dealing with the threat.
Agatha and Bruno are more nuanced cases -- Bruno himself isn't actually all that evil, nor does he really care about the group's mission too much. Rather, he seeks strong partners for battle, and as a result, sided with them for the change to become stronger, only for Agatha to take advantage of that simple motivation and use him as a human experiment for the power of the badges. Agatha, perfectly fitting the Ghost-types she specializes in, is highly vindictive and holds a grudge against Professor Oak for leaving their research group and for defeating her in the Pokémon League. Thus, when Lance's ideals prove to work against Oak and his 'dex holders while simultaneously helping the Pokémon, it's easy for her to join up with him. The promise of the power of control is too powerful for her as well, as she uses the power of the badges to control hordes of Pokémon to attack the mainland, and even Bruno when his motivations aren't enough to accomplish their purposes.
As a result, the Elite Four are a group who see themselves as the good guys with an emphasis on an "ends justify the means" philosophy allowing them to do almost anything without it being out of character. While post-defeat appearances would tone done their power and even offer redemption as Bruno takes a spot in the first official Elite Four with other former villains, they served as deadly adversaries for Yellow and the others, challenging not only their strength but their convictions as well.