Two planets rotate each other and are tidally locked. They are where earth is around a star nearly identical to the sun. One planet is much wetter, featuring oceans, swamps, jungles, and forests. The other is much dryer with plains and deserts. Both are about earth-sized and have similar atmospheres. They are close, like, 3,000 miles surface to surface. A moon about the size of ours orbits the two. This system orbits a sun at he same rate as earth. On one lives a race of lizard-men and on the other lives a race of electric eel-men. I'll let you pick which species belongs on which planet. Anyway, they are both extremely sensitive to radiation. Other than that, you can pretend they are human.
Both planets have futuristic technology, so they have all the modern conveniences of earth, and more besides. The lizard people issue an ultimatum. The inhabitants of the other planet must evacuate to their moon colony or face all out war/extinction. They have 1 year, then the lizards will invade their planet and kill everyone. However, the eel-men have prepared for this...
So, how do the inhabitants of one species kill the other ones without destroying the other planet? If one planet is destroyed it throws the other out of its orbit with potentially disastrous consequences. Also, radioactive weapons are impossible to manufacture, because it would kill all the aliens who would make the bombs. Not only this, but these species are similar enough that they are affected by the same diseases. So, how would one civilization wipe out the other and leave both planets habitable? The moon doesn't have to survive, but the planets' orbit must be left mostly unchanged.
Edit - The moon could be unnatural, put there by these alien species. I don't care about the stability of the moon's formation, but there is a sizable body of something that orbits these two planets.