Gio Gonzalez hurled only 68 pitches Thursday afternoon at Nats Park. (Ricky Carioti/The Washington Post)

Clunkers, once a common and expected occurrence, had become an endangered species for the Washington Nationals. They assembled a pitching staff that often dominated, kept them competitive most days and rarely turned a midweek matinee into a wasted afternoon. But those days lurk for every team, no matter their place in the standings. Thursday afternoon, Gio Gonzalez took the mound for a pitcher’s duel and turned in a dud.

In a showdown with New York Mets ace R.A. Dickey for the major league lead in wins, Gonzalez suffered his worst start in a Nationals uniform. As the Mets pummeled the Nationals, 9-5, Gonzalez allowed six runs in 31 / 3 innings. He struck out just two batters, walked two unintentionally and allowed two homers. The duel fizzled, the Nationals lost a chance to sweep, David Wright smashed two homers and Gonzalez skulked off the mound after 68 pitches.

“I just felt a little flat,” Gonzalez said. “Nothing was moving too much. You’re going hit some patches every once in a while. You leave anything out there, they’re going to make you pay for it.”

Gonzalez established himself as an early-season Cy Young candidate and made the all-star team, but in the past month he has fallen off that torrid pace. In his past nine starts, a span that started June 3, Gonzalez has a 4.93 ERA. Manager Davey Johnson saw no big-picture reason for concern.

“It was one of those days. He didn’t have too much command,” Johnson said. “He didn’t have too much going for him. Command is the big key for him. It was one of those days. I don’t think he had his best stuff, either.”

Friday, the Nationals will begin perhaps their most crucial series since baseball returned to Washington in 2005. The Atlanta Braves, after beating the Giants on Thursday afternoon, will come to Nationals Park trailing them in the National League East by 3½ games. By the end of a four-game series, which includes a Saturday doubleheader, the Nationals could either hold a dominant lead or stand in second place.

“I wasn’t looking ahead,” Johnson said. “But I’m sure some of the guys were looking ahead a little bit.”

Even though the Nationals had little chance Thursday after falling behind by eight runs after four innings, Johnson said, “it’s not always a complete bad day.” They rallied enough to have the tying run in the on-deck circle in both the eighth and ninth innings. Bryce Harper came to the plate down five with the bases loaded in the eighth, flying out to left. The Mets used four relievers for the final five outs.

Drew Storen unveiled a new-and-improved sinker in his season debut, a 1-2-3 ninth. Ian Desmond slapped a pinch-hit single and convinced Johnson he’s fit to return to the lineup Friday. Henry Rodriguez pitched a flawless 11 / 3 innings, and Mark DeRosa came off the bench with two hits. Rookie catcher Sandy Leon replaced Jesus Flores and roped his first major league hit, a single up the middle. “Amazing,” Leon said. He will send the ball to his father in Venezuela.

“A lot of good things happened in that ballgame,” Johnson said.

Still, they will have to hope their performance against the Braves goes better if this was the dress rehearsal. As Gonzalez faltered, his defense conspired against him. Andres Torres, the second batter of the game, rolled a routine grounder to second baseman Steve Lombardozzi. A natural second baseman, Lombardozzi has dutifully played out of position in left field most of this season.

Back at his old position with Desmond out, he has shown some rust, making awkward transitions from glove to throwing hand. With Torres ripping down the line, the slow transfer made Lombardozzi’s throw arrive just late. Torres was on first with a preventable single.

Perhaps still thinking about Lombardozzi’s gaffe, Gonzalez threw Wright, the next batter, a 93-mph fastball over the heart of the plate. Wright hammered the ball over the visitor’s bullpen in left field, giving the Mets an instant 2-0 lead.

“He did his job,” Gonzalez said. “I left a fastball right down the middle, and he did what a good hitter does.”

Gonzalez allowed only one home run in his first 14 starts, but regression has caught up to him. The weather has warmed and allowed the ball to carry better, and his command has flagged a bit. Ike Davis added to his woes to lead off the second, smashing a homer center. In his past five starts, Gonzalez has allowed five homers.

The Mets kept drilling Gonzalez in the third, a double by Torres, a walk to Jason Bay and a single from Davis that fell in front of left fielder Michael Morse. Gonzalez trailed, 5-1, as the fourth inning began.

He promptly walked light-hitting catcher Josh Thole on five pitches, all fastballs. It was a clear sign the ball would not go where he wanted. After Dickey laid down a sacrifice bunt, Johnson ambled to the mound. After 68 pitches, Gonzalez was done. Johnson instead called on Craig Stammen.

“I’m not going to let him get beat up,” Johnson said. “I’m not going to let him stay out there just to save my bullpen. I’m going to save him.”

As Gonzalez walked slowly off the mound, squeezing his glove with little expression on his face, Johnson asked Flores about his performance. Flores told him Gonzalez was not sharp and missed spots all day. “Not like usual,” Johnson said.

Stammen jogged in from the bullpen to begin a 31 / 3-inning stint that kept the Nationals’ bullpen fresh for the Braves. The first batter he faced, Ruben Tejada, roped a single to center.

Thole slowed around third, but Roger Bernadina booted the ball and it trickled away from him, allowing Thole to score with ease. And then with Thole crossing the plate and Tejada standing at first, for reasons known only to him, Bernadina fired the ball into third base.

Two batters later, Wright smashed his second homer, a three-run blow to center field, and the Mets took a 9-1 lead. Johnson began pulling starters. They could rest up for the most important weekend for the Nationals in years.