There have been a lot of villains that have popped up in the nearly 10 year span of the Arrowverse. And I want to briefly talk about what I believe to be the best.
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Reign - Admittedly, she was more of a physical threat, taking orders from someone else. But as physical threats go, she was epic. She even almost killed Supergirl! That’s got to count for something.
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Neron - While not the most complex, he was one of the more unique villains. The most intriguing thing about him being his relationship and reptoire with John Constantine. He was also a very charming and entertaining character to watch on screen.
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Damien Darhk- The truth is that this villain was introduced on the wrong show. He just felt out of place on the relatively grounded “Arrow” show as the Season 4 villain. But “Legends of Tomorrow” managed to redeem him in multiple ways and became one of the most humorous characters.
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Zoom - Again, not one of the most complex, but he is one of the most intimidating. His costume was fairly terrifying. Even when he was taken by the Speed Force, they still used him as a servant that popped up every now and then.
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Diaz - They REALLY fumbled on this character’s introduction, serving more as a minor villain during the first half of season 6. But after that, he became a true force for Oliver. He even had to make a deal with the FBI in an effort to get him (which failed) that resulted in his identity being known and being sent to prison. Kept him a few episodes too long in Season 7, but his role then was still great.
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Malcolm Merlyn- He served as the first big bad in “Arrow” Season 1. The father of Oliver’s best friend, he would leave a lasting impact and show up several more times in the future as a reluctant ally that would still usually try and betray Oliver.
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Deathstroke- Started as allies and friends before things took a turn for the worse. He caused literal chaos for Starling City and he would destroy a good chunk of Oliver’s life in Season 2. He has returned and is more of an ally again, but his impact is undeniable as a villain.
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Lex Luthor - He is the highlight of “Supergirl” Season 4, even for people who aren’t fans of the show. It is still unclear just how much of an impact he will have, and it is unclear if/when he could return if at all. But unless something huge happens next season, this man can’t be topped in Supergirl’s world.
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Prometheus - He emotionally and mentally broke Oliver, even if it was just for a short while. Everything he did continues to leave a huge impact on how Oliver conducts himself.
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Reverse Flash - The most terrifying villain is the one you can never truly beat. Barry can never stop him from killing his mom. He can never not unlearn all of the skills that Thawne taught him because those abilities are what allow him to be a hero. Yet, he will always be the darkness that looms above his head.