Let me get this straight: your central theme is that suffering is necessary for the good life. Sadly, the nature of humanity is to misguidedly eliminate it. Realizing this, the now-doomed nihilists of the future inflict this suffering on their predecessors to save the world from the lukewarm fate-worse-than-death. The protagonists oppose these attackers as a matter of course, but nonetheless believe in a strikingly similar ethics. A game presumably follows.
I think it could work, and without glossing over the philosophical implications. But what you need to think about is how the game's central dialectic can be embodied in your characters, plot, and gameplay. And if I'm reading you correctly, this is where you're having trouble.
For characters, I would think about the tension between suffering and happiness, and try to distinguish different ways your characters might conceive it. Are there people who believe in hedonism, that the people of the future live the most blessed of lives? Are there people who are willing to concede (or logically should) that the antagonists are in the right? Then think about why these potential characters have their beliefs, both in the sense of how they acquired them and what reasoning or emotions they use to justify them. (Even if you think they're wrong, try not to make them strawmen.) Then think about whether/how these beliefs shape their lives and personalities. When these character ideas become distinct enough, you should find yourself falling in love with a few of them. Or better, falling in love with the harmony between a them. These (or some of these) will be your main characters. Think of how these characters might change over the course of your story. You don't need many character arcs, but it's usually wise to have a couple. Give these characters backstories, relationships, names. Talk to them, and have them talk to other characters to try to get a feel for them.
I sometimes think of plot as a kind of inquiry. Each scene is like an experiment, and the way it plays out reveals something about an underlying dramatic question. Perhaps we come to see some sub-problem that needs to be solved before the question, or a part of the question is resolved. The dramatic question is intimately tied to the theme; to borrow from the Aristotelian idiom, the theme is the universal of which the dramatic question is a particular. The answer to the question embodies the theme, and this is picked up on by the discerning player. The simplest statement of the question might be "will the eternal war be stopped?", and the answer may be along the lines of "yes, because the antagonists' actions are unjustifiable" or "no, because humanity can't escape anomie." It's clear how these reveal the theme. An individual scene might begin with a provocative scenario: the protagonists confront the antagonists in the latter's world. Thus, we can see how the antagonists live, and hopefully the how will illustrate why it's so undesirable.
As for gameplay, I'll offer this advice, and you can work out why I'm giving it. Make the game hard.
I hope this helps. The characters, the plot, the setting, the gameplay, even individual lines and actions -- everything in a story is an interesting, imperfect instance of what it represents. Writers are told to show, not tell, because concretes make what could be impersonal, tense and instinctively relatable.