On Saturday, Washington Nationals General Manager Mike Rizzo ran into Stephen Strasburg’s dad, who was in Phoenix to watch the team play the Diamondbacks. Jim Strasburg braced Rizzo with the same question as the rest of the baseball world: What’s the deal with ending my son’s season — protecting his arm even though he feels perfectly healthy — because of some voluntary innings limit that Rizzo has chosen?

“Mr. Strasburg, don’t ask the question if you don’t want to hear the full answer,” Rizzo replied. “I want to hear it,” Strasburg’s father said.

The answer takes a long time. It includes decades of statistics on rehabilitation from Tommy John surgery and how annual “innings load increases” have led to disastrous re-injury in the past.

It includes the view of the surgeon, Lewis Yocum, who’s performed all the operations on Nats pitchers in recent years. It is Yocum’s belief that pitchers who break down from premature returns from elbow surgery — sometimes ruining their shoulders, and their whole careers, rather then their new elbows — don’t usually do so during the first big stress year but rather the following season. That would be 2013 in Strasburg’s case.

In the end, Rizzo gave Strasburg’s father a list of all of the smart people who disagreed with his innings shutdown limit. “Even my dad says, ‘Let him pitch,’ ” said Rizzo, whose father, Phil, is a lifelong baseball scout.

Then Rizzo said he told Strasburg’s father that the decision to shut his son down was “mine and mine alone.”

“It’s not on Davey Johnson or Mr. Lerner. It’s on me,” he said. “I know it may stain my reputation or my career. There’s no way it can ever be proved if I was right. The easy thing for me is just to do nothing. But I’m hardheaded. The decision was made five months ago because it was the best decision for Stephen and the Nationals. And nothing is going to change it.”

What was Jim Strasburg’s reaction? “He said, ‘That makes a lot of sense,’ ” Rizzo recalled.

With that ice broken, Rizzo told the senior Strasburg that the two worst days of his career were when he had to tell Jordan Zimmermann and Strasburg that they would need career-threatening Tommy John surgery and, best case, each would miss a full year. “Your son’s tough, but he cried like a baby in Philadelphia when I told him,” Rizzo said. “I promised you when I was in your house trying to sign your son that I would take care of him. And I’m going to do it.”

Under cover of the Strasburg shutdown controversy, the true story of the Nationals is being missed. The real narrative, which the Strasburg fuss illustrates, is that the Nats are an organization with enormous self-confidence and, when necessary, defiant indifference.

One reason the Nats have come so far, and so fast, is the same reason they will shut down Strasburg when Rizzo decides the day. The Nats do things their way — or, rather, Rizzo, Johnson and Lerner’s way. They act in line with their best baseball, medical and philosophical judgment. Then, they don’t care what anybody thinks — as they’ve proved time and again in recent years, though few notice.

Look at all the instances where the Nats, as their fortunes started to turn, have ignored pundits or fans, mocked conventional wisdom, defied the guidelines of the commissioner, irritated their foes’ feelings or taken the tough-love approach with young prospects.

With “Moneyball” barely out of theaters, they are already several years down the road of giving scouts a “65-35” say over stat nerds in their decisions. “Creating those Sabermetric stats was smart and hard. But, come on, how tough is it to grasp that stuff once every team’s got it? Even I can understand most of it,” Rizzo joked years ago. “We’ll lean a different way.”

Who do you draft or sign as a free agent? How much do you pay? Why would you risk a 19-year-old in your lineup every day? Why don’t you want Adam Dunn, at any price, or Prince Fielder for a market price? Whatever the majority thinks, the Nats tend to disagree.

When the Nats were considering Johnson for manager, they passed around a story that described Davey as iconoclastic, outspoken and a manager who loved to run a club that, at times, felt like a studious pirate ship. The Nats, none more than Rizzo, thought that made Davey ideal.

Everywhere you look, the Nats bend the norms. They signed amateur free agents Strasburg, Bryce Harper, Anthony Rendon, Matt Purke, Alex Meyer and Brian Goodwin for record prices, sometimes shattering previous marks by 50 percent or more. Lerner gave the “go” and Rizzo executed.

When MLB changed those rules, the Nats still blew up the new slot system this year by drafting “unsignable” Lucas Giolito — the teenager with the 100-mph fastball. They convinced him he’d be happy as a Nat and, come hell or high water, they’d treat his already sore elbow with as much respect and restraint as they had Zimmermann and Strasburg. He signed.

Few thought Jayson Werth was worth $126 million, especially when much of the money was to bring attitude, swagger and professionalism. Now the Nats have swagger, Natitude and professionalism.

Everybody, including me, thought they should sign Dunn and Josh Willingham to multiyear contract extensions in 2010. Both are having big years, but Rizzo wanted better defense along with his offense. He got it.

Everybody, including me, said they should sign free agent Mark Buerhle and, if they failed, deal for a well-known veteran starter like Zack Greinke. Instead, they traded four prospects for lesser-known, joyful Gio Gonzalez, who has been exactly the vibrant personality that the Nats needed to enliven their gifted but dry-to-droll rotation.

When Manager Jim Riggleman pulled a midseason stickup for a contract extension, Rizzo let him quit. He talked Johnson back into the driver’s seat and took heat for his insensitivity toward the hometown Riggleman. Yes, 14 months ago, Rizzo was called a short-fuse bumbler.

At least once since he became GM, Rizzo was so peeved at ownership for ignoring his advice that, according to a reliable source, he said, “If you don’t do this, I’ll make you fire me.” Told the Lerner family loved the job he was doing, Rizzo responded that the owners had misunderstood his words. He said he would make them fire him; and they would have to pay his whole contract, because he wouldn’t quit. The deal got done the next day.

In the current Strasburg angst, the key point is missed. The Nats take stands, based on what they believe.

There are many ways to run a successful sports franchise. All of them work, if done with consistency and conviction. None work without it.

All of the Nats’ decisions won’t be correct. But every call they make is now based on one standard — what they think is best for the Nats. Not on how it “plays.”

The Nats haven’t even finished their first winning season. But they have one key ingredient of franchises that build wisely, behave consistently and foster loyalty: bedrock stubborn conviction, mixed with a dollop of disdain.

For previous columns by Thomas Boswell, visit washingtonpost.com/boswell.