NEW YORK — Jeff Nichols’ “Midnight Special” — a sci-fi mystery that plays out in a clandestine, nocturnal chase from Texas to Florida — began with an idea of light in the writer-director’s mind, and a desire to recapture the cryptic thrill of science-fiction films like “Starman” and “Close Encounters of the Third Kind.”

But it wasn’t until after Nichols, the 37-year-old writer-director of “Mud” and “Take Shelter,” was driving to his writing office in Austin, Texas, one day when he knew what “Midnight Special” would be about. That was when he heard the news of Sandy Hook.

“This movie, it’s a silly sci-fi chase movie, but at its heart is me trying to deal with that: Pulling over to the side of the road and hearing about children being shot and picturing my son being afraid in his final moments and just being devastated,” says Nichols. “Does the movie reach those heights? Probably not. Is it good that it doesn’t? Maybe. But this is what I was feeling.”

“Midnight Special,” which Warner Bros. will release Friday, is the first studio film for Nichols whose films — personal tales rooted in classically American moviemaking — have made the Arkansas native one of the most exciting voices in independent film. “Midnight Special” finds him developing his command of special effects in a bigger budget production than he’s done in the past, yet remaining a steadfastly sincere storyteller.

“The thing that Jeff possesses in spades is if you carved his heart out, I’m sure it would be heavier than most people,” says Joel Edgerton, a co-star in the film. “He feels things very deeply. His films are infused with an emotion that generally trends toward family and love and protection and care. Even if there’s violence, it’s because it’s spurred on by the lack of those things.”

In “Midnight Special,” Michael Shannon (who has appeared in every movie by Nichols, beginning with his debut, “Shotgun Stories”) stars as the father to 8-year-old Alton (Jaeden Lieberher), a boy who possesses a mysterious special power. Alton, who wears goggles to cover eyes that can illuminate in searing beams of light, has attracted the pursuit of the government (Adam Driver plays a sensitive NSA agent) and the religious sect from which his father is trying to rescue him.

The film, patient but explosive, metes out exposition slowly and leaves some questions unanswered. It opens with a Chevelle throttling through the night, headlights off, with the father and his accomplice (Edgerton) driving with night-vision goggles. Their mission is vague and uncertain, but Shannon’s father is compelled by a faith in his son and a determination to shepherd Alton where he needs to go.

“That’s parenthood,” Nichols, who has a 5-year-old son with his wife, said in an interview over lunch in Greenwich Village. “Just because you believe in something doesn’t mean you understand it. In fact, usually you don’t.”

“Midnight Special” is a kind of companion to Nichols’ “Take Shelter” (2011), which grew out of his anxiety in becoming a parent. Shannon played a paranoid father who sees literal storm clouds on the horizon.

“Fear has been the basis of all of my movies, almost,”’ says Nichols. “‘Shotgun Stories’ was about the fear of losing my brother. ‘Take Shelter’ was the fear of the entire world falling apart and the fear of becoming a parent. ‘Midnight Special’ was the fear of losing my child. But fear in and of itself is not a story. It’s a catalyst that creates something.”

“Mud,” a Mark Twain-esque coming-of-age tale set along the Mississippi and co-starring Matthew McConaughey, was very well received and selected for the Cannes Film Festival. But it struggled to find a distributor and wasn’t much promoted. Nichols grants that the experience “shook my confidence.”

But “Mud” inspired the interest of Warner Bros., which gave Nichols final cut on “Midnight Special.” Speaking positively about his studio experience, Nichols feels emboldened to try a $100 million film, should the right opportunity present itself.

“The reason I’m more interested in it now is: I know what to ask for,” says Nichols, whose crew is populated by regular collaborators like cinematographer Adam Stone, editor Julie Monroe and production designer Chad Keith. “I know what I need to make a film my way.”

Nichols next film, currently being edited, is “Loving,” about the interracial couple Richard (Edgerton) and Mildred Loving (Ruth Negga) whose marriage made them criminals in Virginia in the 1950s. Focus Features will release it in November, placing it the heart of awards season.

“Jeff’s very comfortable around me, but sometimes being comfortable is not the best thing for art,” says Shannon, who has a small part in “Loving.” “It’s not such a bad thing for him to work with somebody like Ruth. It’s a different kind of story for him and it’s good for him to branch out.”

For the ever-progressing filmmaker, “Loving” may be yet another evolution. At the film’s mention, Nichols cups his hands over this reporter’s voice recorder and whispers: “It’s the best movie I’ve ever made.”

“It’s very quiet. It’s very silent. It’s very painful. It’s very beautiful,” he says. “In a time where the political debates around marriage equality and around race are so heated, this film just cuts through it. It’s just about these two people.”