San Diego has lost its premier chronicler, a red-haired transplant who came here as a young sailor in the 1940s and became the most respected journalist in the city he called a “stumblebum with character.”

Through his long career, Neil Morgan tried to figure out what it meant to be a Westerner, a Californian, a San Diegan. He sought to understand what makes us different and why so many Americans are drawn to the Golden State, a place filled with flim and flam, opportunity and ruin, beauty and disaster.

Toward the end of his life, Morgan boldly took aim at the city establishment he’d so eagerly joined. After being sacked by the local paper after a 54-year career, he helped create a small but mighty news organization — this one — designed to shine a light on the city’s darkest corners and help San Diego become a better place.

Morgan died Feb. 1 at his La Jolla home at the age of 89.

Judith Morgan, his wife, said there will not be a service, at his insistence.

“He felt that this city and region had honored him abundantly over so many years. He loved San Diego and San Diegans very much — even when nagging us to do better, fly straighter, rise higher,” Judith Morgan said in an email to our staff.

It’s hard to overstate how big of a personality he was in San Diego.

“In my view, he was the best journalist San Diego ever had,” said his longtime friend Bob Witty, the former director of Copley News Service. “At one point in time, probably before Pete Wilson, Neil was the best-known person in San Diego.”

When he arrived in San Diego as a sailor during World War II, Morgan came in on a “troop train” that pulled past the San Diego station then backed up into it on its return trip to Los Angeles. “This was the beginning of his insight into the spur-track city, a warm pocket in the nation’s lower left-hand corner,” wrote journalist T. George Harris.

Morgan was a North Carolina boy, the son of an outspoken minister and civil rights advocate. (“Can no one silence this old man?” complained one newspaper reader.)

He inherited his father’s commitment to liberal values and preserved a faint hint of the drawl of a down-home country gentleman. In his words, he became a San Diegan through and through, but with an outsider’s ability to see the city’s sun-bleached heart through the gauzy haze.

Morgan got a columnist job at the now-defunct San Diego Daily Journal and began chronicling what he saw. After a few years, he landed at the Evening Tribune in 1950 and didn’t leave until 2004.

In one of his “Crosstown” columns, he wrote a “Love Letter to a Town” — San Diego. He described it as a place with a history, a lazy border town plagued with massacres that later boasted the jewel of Balboa Park and didn’t mind being “second-rate to Los Angeles.”

“They say some towns live in the past,” he wrote, “and some towns don’t know they had one. … But you’ve got one beautiful!”

It didn’t take long for Morgan to spend more time pondering California’s past, present and future. He began writing books and gaining a national reputation as a pre-eminent interpreter of Californians — “these unusual people in this extraordinary place … equipped with vitality and with dreams” — and the West. He wrote articles for major national magazines, chronicled San Diego in a daily column, and married a San Diego Union reporter then named Judith Blakely, who became a well-known travel columnist and author.

Morgan wrote that San Diego offered “the image of a town of unpretentious Midwestern tastes” even as its skyscrapers lurched skyward and its research institutes — he was a big booster of them — shot for glory.

In the 1980s and early 1990s, he was editor of the afternoon Evening Tribune, known for being scrappy and livelier than its staid morning sister paper, The San Diego Union. He told staffers to turn the Trib into “America’s most sophisticated country daily.” The paper’s journalists “smiled and scoffed,” he wrote, but they remembered what the phrase “implies about a people-oriented, caring style of newspapering.”

With Morgan at the helm, the Trib won a Pulitzer for editorial writing, only the third to ever go to a San Diego newspaper until that time. (The Union never won one, a fact that Morgan surely relished.)

But, as historian Kevin Starr writes, Morgan was hardly an outsider throwing rocks at the patrons of the city’s business meetings and high-end cocktail parties. He was “part of the establishment — a long-term Mr. San Diego — and a tireless socializer on the La Jolla scene.”

Indeed, Morgan was actually named “Mr. San Diego” by the Rotary Club in 1999 and lived in La Jolla. In his column, a daily compilation of brief tidbits, he often wrote about San Diego’s glitterati — the jokes they made, the things they did, the places they went.

He hobnobbed with San Diego’s celebrities, from mystery author and screenwriter Raymond Chandler and Theodor “Dr. Seuss” Geisel to Roger Revelle, the father of UCSD.

As the 20th century began, Morgan was an associate editor and metro columnist at The San Diego Union-Tribune, the product of a 1992 merger between Tribune and Union. He had the perfect catbird seat to watch the new era unfold as his career began to wind down.

But then Morgan turned against the establishment and it — at least in the form of its major daily newspaper — turned against him.

For reasons that are still unclear, the Union-Tribune fired Morgan in 2004. It surely hadn’t helped that he’d become increasingly critical of the city’s power structure amid a series of scandals that exposed corruption and incompetence at the highest levels of City Hall.

As he left the newsroom, the newspaper’s staff gave Morgan a standing ovation.

Annoyed by the newspaper’s failure to fully uncover the city’s decline, Morgan met with his friend Buzz Woolley, a wealthy entrepreneur who later told a journalist that Morgan “was the last one at the newspaper who would write anything critical about what was going on.”

Morgan saw a city besieged by selfishness and “gimme-gimme lobbies at City Hall,” unable to come together or even comprehend how bad things were getting. “The world had a glimpse of us as the rubes that we insist we are not,” he later wrote in a piece about the monumental pension scandal that nearly took the city down (and still might).

Woolley and Morgan founded Voice of San Diego, an online news organization that would be devoted to investigative journalism.

“Neil passionately loved San Diego and journalism. As co-founder of Voice, he leaves a lasting legacy that reflects his passions,” Woolley said.

Voice of San Diego turns 9 years old in just a week and continues its mission of shedding light on San Diego — the good and the bad — while serving the citizens of this city and county as they strive for a better community.

In journalists young and old, Morgan left a legacy of commitment to truth — even if it’s painful and hits close to home — and an understanding of how the past affects the present and future.

“News reporters have been taught that their highest calling is helping to create a sense of community tolerance and understanding in a city that has grown too fast to recognize itself,” he wrote on the last day of the Tribune’s existence in 1992. “To do that means providing an accurate and insightful image each day of what San Diego was that day, and also what it might become.”

A fine mission to match a fine legacy.