We love superheroes, but most of the time what makes a superhero movie work is the supervillain. Just as the Avengers on the other side of the Marvel Universe move into X-Men territory by having the supes fight each other, with a villain in “Civil War” who is a mere human, with the most human of motives and goals rather than Loki’s “let’s blow up the universe and roast marshmallows on the flames” sort of threat, the X-Men, whose primary plotlines rest on the shifting loyalties of its mutant members, switches direction toward a more Loki-esque bad guy.

That would be the first mutant of all, going all the way back to ancient Egypt, where he was a god. He is resurrected, he is nearly omnipotent, and he is played by one of the most exciting actors in movies, Oscar Isaac. But there are three big problems with Apocalypse, and that means there are three big problems with the movie.

First, we never really understand that “nearly” part about his powers, and therefore we cannot judge the threat he poses in any given confrontation. Second, Isaac is a superb actor with deeply expressive eyes and voice. Yet he is put into a mask that conceals his eyes and given a double-tracked distortion of his voice. The big, hulking outfit also impairs the precise, distinctive physicality he has brought to roles as different as “Star Wars” ace Po Dameron, the title folk musician of “Inside Llewyn Davis,” and billionaire Nathan Bateman (“Ex Machina”). The power of his presence as a performer is all but muted just when we need a character to be terrifying.

Plus, we’ve seen ancient Egyptian super villains before. After the many versions of “The Mummy,” we need something more than he’s from the time of the pyramids plus chanting. But there is a very cool opening sequence that brings us through history to 1983, the pre-digital era when overhead projectors in classrooms represented cutting-edge technology. And Magneto seems to have found peace, in a small town, with a factory job, and a loving wife and daughter.

Of course, that can’t last. And soon he has experienced yet another devastating loss, and returns to his bad, furious, destructive self — until someone who is even more furious and destructive comes along.

When I say that this episode is a “Muppet Babies” take on the X-Men, I do not necessarily mean that in a bad way. Origin stories are intriguing, and the X-Men have always had an adolescent quality, with the onset of their mutant powers coming with puberty and acting as a heightened metaphor to examine the sense of uncertainty, anxiety, and isolation that comes with the physical and emotional changes that separate teenagers from their childhood. It is intriguing to see Scott (Tye Sheridan) rubbing his red eyes as he becomes Cyclops. But Sophie Turner does not have the screen presence of Famke Janssen as the young Jean Grey, in part because her telepathic gift is not as cinematically dynamic.

Quicksilver (Evan Peters) once again provides the high point, not just in a darker showpiece callback to the sensational Pentagon kitchen scene in the last film but in the film’s brief but most emotionally authentic scene, involving his relationship to Magneto. In a movie about mutants with superpowers, the best moment is human.

Parents should know that this film includes extended comic book-style action violence, with characters injured and killed and some disturbing images, skimpy costumes, and some strong language.

Family discussion: What is the biggest challenge in getting the X-Men to work together? Which powers would you like to have?

If you like this try: the other X-Men movies, especially “Days of Future Past”