“Weathering With You” begins with a protagonist who also decides to put some distance between himself and his past. That protagonist is high school student Hodaka Morishima (Kotaro Daigo), who runs away from his small island hometown to Tokyo.

From the towering skyscrapers of Shinjuku to the low-rise, shrine-dotted neighborhoods of the east, the rain-soaked metropolis is captured in breathtaking detail.

Location hunting for the film took about two months.

“The topography of Tokyo is important to the film,” Shinkai says. “There are actually parcels of land near Tokyo Bay, for example, that are lower than sea level. That plays a part in the story, so it was important to do that research.”

Shinkai believes the attention to detail should help viewers connect with the story.

“I want people to feel as if this is something taking place in our world right now,” he says. “It’s not a piece of fiction that has nothing to do with you and I — it’s happening here and now.”

Hodaka spends his first few days in Tokyo in awe of his new surroundings, wandering the streets of Shinjuku in fear and wonderment.

Shinkai, who was born and raised in Nagano Prefecture, had a similar reaction when he first visited the metropolis.

“I came with a friend after graduating high school,” he recalls. “I must have been 18 years old. We walked around (the Shinjuku entertainment district of) Kabukicho in total fear. Various people approached us, from religious groups and adult shops. … It was pretty scary (at the time).”

“Back then, the Tokyo Metropolitan Government Building was brand new,” Shinkai says, referring to Shinjuku’s iconic twin towers. “It was a huge, shining skyscraper. … It felt like a city of the future.”

After two decades living in and around Shinjuku, Shinkai still finds himself fascinated by the capital’s urban landscape.

“Tokyo is covered in dark asphalt and when it rains, it turns almost black,” he says. “The man-made lights of the city reflect against that darkness. And when a ray of sunlight hits the damp asphalt, it sparkles. You might typically think of wet asphalt as pretty drab, but I think it’s beautiful and I want viewers to experience this as well.”

The few rays of sunlight that appear in “Weathering With You” come courtesy of the film’s female protagonist, Hina Amano (Nana Mori), who discovers that she is able to create a reprieve from the rain through prayer, causing the sun to shine in a localized area for a few hours. In short, Hina is, as one character refers to her, a “100 percent fair-weather girl.”

Shinkai, who studied literature in college, is an avowed fan of novelist Haruki Murakami. Might he have taken inspiration for Hina from Murakami’s “On Seeing the 100% Perfect Girl on One Beautiful April Morning”?

“I was definitely conscious of it,” says Shinkai, laughing. “There’s no real connection as such, but you might make that leap if you’re a fan of Murakami. I do love that story and it just came out naturally.”

Shinkai explains the Murakami links — conscious or otherwise — go even deeper.

“I didn’t realize this as we were making the film but, in hindsight, it’s actually quite similar to Murakami’s ‘Kafka on the Shore,’” Shinkai says.

Both the main character of that 2002 novel and Hodaka are teenage runaways who meet a mysterious cast of characters; both works of fiction even feature fish falling from the sky.

“It’s possible I unconsciously remembered that novel,” he says. “However, I do believe that when you break down stories, they all ultimately end up following a few basic structures.”

Shinkai turned 46 this year. Aside from a few errant gray hairs, you might peg him as a decade younger — not just because of his boyish grin, but because of the way his young characters seem to reverberate with audiences at home and abroad.

But when I ask Shinkai whether he thinks the young people of Japan will sympathize with the themes of this latest film, he pauses.

“I’m not sure,” he says. “I’m not so young anymore.”

That may explain why “Weathering With You” features Shinkai’s most three-dimensional adult character to date, Keisuke Suga (Shun Oguri), a writer who takes Hodaka under his wing and whose complicated family issues are fleshed out in a significant subplot.

“First and foremost, the story is about Hodaka coming into conflict with society, so I needed an adult to represent society as a whole,” he says. “That’s Suga’s role. But, indeed, he’s about my age and he has a young child — just like me.”

By including this grown-up in the narrative, Shinkai was able to explore his own thoughts on adulthood.

“When you get older, you accumulate more ‘things’ that aren’t easy to let go of, whether that’s work or family or what have you,” he says. “The main characters of the film are still a boy and a girl, but a middle-aged guy naturally worked his way in there as well.”

While the director insists “Weathering With You” is primarily entertainment, adulthood is just one of the deeper themes he explores. The relentless rain depicted in the film, for example, was partially inspired by the extreme weather events of the past few years.

“Japan used to have four distinct seasons, and that was a source of pride here,” says Shinkai, whose “5 Centimeters per Second” takes place around the cherry blossom season.

But in recent years, he says, “weather has become something hostile to humans, something we have to prepare against. It’s frightening.”

In “Weathering With You,” Hodaka visits a shrine where a monk scoffs at the notion that, historically speaking, there’s anything particularly abnormal about a long rainy season.

“Humans think on a scale of 100 years or so, but the world works on a much larger scale,” Shinkai says. “That’s what the monk is saying — humans can’t control the weather. That’s one way to look at things but, at the same time, that’s not quite right either, as humans have definitely changed the weather. I don’t come to a clear conclusion on this but the issue definitely lies at the heart of the film.”