There is a norm while writing any story. The antagonist is supposed to be stronger or at least as strong as the protagonist. In science-fiction, the story is different. The antagonist can be god-like and impossible to defeat. It can also be a tiny, microscopic organism which can be crushed by foot and yet has the power to control most of the beings on earth. The quintessential science fiction antagonist is not bound by parameters. Rather, its limitlessness is quite the reason why it becomes problematic for new authors to create an accurate one. There have been many articles regarding how to create an antagonist for just about any novel. That needs to be followed but in matters of science fiction, there needs to be specific things to be talked about.
Before trying to demarcate how a science fiction antagonist should be, we must check what a science fiction antagonist should not be. The science fiction antagonist should not be omnipotent or infinitely powerful than the protagonist. Such heroes in the realm of science fiction have been highly overrated of late. The average reader may not have read science fiction novels. He or she may have the idea of Thanos of MCU or the dinosaurs of Jurassic Park in their head. To have continued idea of an infinitely supreme hero might come as a cliché example. You may start with building a powerful force to be reckoned with but make sure this should not be as powerful as the devil himself. and continue describing about their humane aspects, their weaknesses and so on. And make sure, these weaknesses are the reason for their downfall.
Secondly, one needs to learn to do is avoid stereotypes. More than any other genre, it is science fiction which deserves a blatant change when it comes to the antagonists. Every time we have a corporation antagonist, the evil capitalistic society is on the radar. Same goes for the common antagonist: the kind of person we face every day for example, a psychopath. Such characters come off as weak sci-fi antagonists. One may look into the possibilities of having an everyday antagonist. Sure, there is no hard and fast rule for anyone to stick to rules and not create infinitely strong antagonists. One can. It should look original and not a plagiarized idea from the best science fiction novels and stories. The reason why it is best avoided is: at the end of the day, everyone has more or less similar ideas about God or creator or omnipresent/omnipotent entities. And we tend to imbibe the similar characteristics in the antagonist.
The third and the final rule would be to have an idea of how potent your antagonist should be. The antagonist may be of the size of the toy. It maybe from a species which is considerably weaker than the humans. At this point, the author should ask: what are the aspects which make this species considerably strong than the protagonist. Rather than going the other way round, one can maintain a suspense. You can reveal the degree of antagonist’s power earlier and as the story progresses, you can show their vulnerability or his side of the story in the last two or three chapters.