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Let's say you have two sides who are basically no better than the other. Both are criminals with no redeeming qualities, and both are at war. Think COBRA and HYDRA going to war.

They both have plans for world domination and are ruthless in their pursuit of it, willing to kill or corrupt anyone in their way. With both sides being evil, it would be hard to root for one over the other. The audience may get bored with this since there are no good guys, and the world will suffer regardless of who wins.

How can you make a setting like this interesting and keep your audience engaged?

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    That is, you have no idea what to write and want us to come up with a story for you? – user29032 Apr 20 '18 at 5:08
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    It looks like you want us to come up with a story and tell you what you should write - which is not what this site is about. We can help you with specific problems, but just putting a High Concept (WorldBuilding Meta) out here and asking us what to do now is not going to give you the answers you want. If you don't know what to do with your idea store it away somewhere and come back to it later when you know what you want to do with it. – Secespitus Apr 20 '18 at 7:26
  • I think this question is on topic, and has very good on topic answers – Andrey Apr 20 '18 at 19:10
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I would think that the main thing that keeps the readers interested are the characters. Even though these characters might belong to an evil organization, they might be redeemable themselves. Or even if they aren't, they might be interesting.

Also, what appears to us as an evil organization, may appear to those inside as an organization that has good goals. Perhaps they believe that by taking over the world they can save us from ourselves. For example, by forcing through a world government, they might believe that they would be able to reverse global warming and prevent war and terrorism.

Why is the protagonist a member of this organization? He might have different reasons that the organization itself. Perhaps the organization started out with good goals but became corrupted. The protagonist might start out trying to clean up the corruption, but become corrupted himself.

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Both are criminals with no redeeming qualities

There's your problem. You have a pair of one-dimensional cartoon supervillains who are evil just because. Those kinds of villains are unrealistic and, these days, tend to be less well-received than more nuanced villains. And in describing them, you've focused only on their similarities.

Focus on what makes them different. Give them different motivations, and different personalities. Make them stand out from one another. You readers certainly aren't going to root for one side over the other if they can't even tell which side is which.

A good example, off the top of my head, is Pokémon Emerald, where you have two opposing groups of villains: one wants to create more landmass, the other wants to create more ocean. It's not their intentions that make them evil, but their actions (stealing Pokemon and equipment, battling anyone who gets in their way, unleashing ancient kaiju, etc.). They have distinct uniforms and personalities, and the conflict between them stems from the fact that their goals are diametrically-opposed.

You already have a reason for your groups to oppose each other: they both want to take over the world. Give them different reasons for wanting to do so: maybe one believes they're freeing the masses from tyranny and oppression, while the other believes people are too stupid to be relied upon to govern themselves properly. Give the mooks different reasons for wanting to be part of these groups - they aren't going to be hiveminds, after all.

A final note suggestion would be to focus on the conflict itself, and not the potential consequences if/when either one wins. If the conflict is compelling enough, readers will be enjoying it enough that they won't worry about what might happen afterwards.

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You can have fun with it.

For example, "Invader Zim" is, most of the time, evil vs. evil, but it's all humorous, so although you recognize Zim winning is bad, you don't mind so much.

Also, you can take advantage of tropes to be a little more serious, but keep enough humor to distract the reader from dwelling too much on the thought of how bad they are. Hydra bad guy, for example, could kill one of his minions every meeting, just to prove how bad he is. The minions have figured it out. To keep themselves alive, they scheme to get one of their group "selected" as the likely target next time they meet with the boss. The minions might have discovered Hydra commander prefers to whack people wearing a red shirt, who work in security, or who haven't figured out how to insert their names into the conversation (thus providing themselves character immunity). You can make indirect commentary about the stereotypes of villains that the reader gets, but goes over the heads of the characters.

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