Nationals right-hander Nate Karns sits in the dugout after being pulled from his second major league start. He struck out six in 4 2/3 innings but allowed four runs (three earned). (ERIK S. LESSER/EPA)

The storm clouds rolled over Turner Field around the fifth inning Sunday afternoon, sidling next to the figurative darkness already looming above the Washington Nationals. The Nationals, with a roster held together with twine and safety pins, headed toward another forbidding milestone.

Widely recognized as a World Series favorite two months ago, they handed the ball Sunday to a rookie making his second career start. In the corner outfield spots stood a first baseman and a second baseman. They had eight relievers, four bench players and no starters batting above .288. They asked that crew to keep them from tumbling below .500.

As thunder clasped in the latter innings of their 6-3 loss to the Braves, the Nationals dropped to 28-29, a season-high 61 / 2 games behind first-place Atlanta. Nate Karns allowed four runs (three earned) in 42 / 3 innings, and the patchwork Nationals behind him offered little support. Ian Desmond drilled a solo homer, but the Nationals managed only five hits for the second straight game.

Reliever Zach Duke allowed a bases-loaded double to Freddie Freeman in the sixth that gave the Nationals a three-run deficit. The Nationals had not come from three runs behind and won all year, and Sunday offered even less hope. In 10 games against the Braves this season, the Nationals have not scored a single earned run against their bullpen.

“We deserve to be where we’re at right now,” first baseman Adam LaRoche said. “We’ve played like crap. Still not in awful shape. We’re pretty deep into the season. We’ve got to get it going or else we won’t be there in the end. I don’t sense any panic or anyone stressing over it, but it’d be nice to pick it up a little.”

After facing some tough opponents in the Orioles and Braves, the Nationals will face five teams with a combined record that is six games under .500. The Post Sports Live crew discusses if this will help the team’s performance. (Post Sports Live)

The Nationals could cull through the wreckage of their 10th loss in 15 games and find few silver linings. Right fielder Jayson Werth will rejoin the Nationals on Tuesday after missing an entire month with a strained hamstring. Sunday, he finished a five-game minor league rehab appearance at Class A Potomac with two three-run homers.

“He must’ve been really feeling frisky,” Manager Davey Johnson said. “He’ll be ready to carry us on his shoulders, I’m sure.”

In his major league debut, Erik Davis pitched out of a two-on, no-out jam and retired all five batters he faced. When Washington returns to Nationals Park, the lowly New York Mets and Minnesota Twins await.

“We’re in it for the long haul,” Desmond said. “It’s not a sprint. It’s definitely a marathon. You don’t want to be the guy that runs the first 100 yards as fast as you can and runs out of breath towards the end. Obviously, we’re not playing a full squad here, but we’re managing to stay in ballgames. That’s really all you can ask for.”

When the season started, the Nationals were not supposed to fall back on silver linings or take a back seat to other contenders. The Braves are now 7-3 against them after taking another series. The Nationals scored seven runs all weekend in Atlanta, below their season pace of 3.46 per game.

When the Nationals took the field Sunday, the bottom three position players in their lineup were hitting .144 (Tyler Moore), .160 (Danny Espinosa) and .143 (Jhonatan Solano). By game’s end, having drawn no walks to go with their five hits, the Nationals’ team on-base percentage dropped to .287, lowest in the majors and prospectively the fifth-lowest of any team since divisional play began in 1969.

“Just about half the ballclub is not doing the things they’re capable of offensively,” Johnson said. “I look up there, a bunch of guys are hitting .150. There’s too good of quality players here to be doing that. I’m sure we’ll pick it up. It’s just a tough time. Couple guys hurt, that always gives opportunity for other guys. We have talent. We’re just not getting it done.”

Karns’s first pockmark arrived at the outset. Andrelton Simmons led off with a grounder to third, and Ryan Zimmerman heaved the ball across the diamond in the general direction of first base. LaRoche scurried off the bag and caught it on the run, about five steps toward the outfield grass. Simmons had reached on Zimmerman’s 10th error of the season.

On the very next pitch, Ramiro Pena hammered Karns’s 92-mph fastball into the right field bleachers. The Nationals’ hope to quickly erase the sting from Saturday night’s walkoff loss evaporated, and the Braves had taken an instant 2-0 lead.

The Nationals tied the score off Paul Maholm in the second with three straight hits from LaRoche, Desmond and Moore and a needed break — Maholm dropped what would have been the third out as he covered first base on Karns’s sharp grounder to first.

Karns said he felt more relaxed making his second start, but he would relinquish the lead in the bottom of the inning, when B.J. Upton smoked a solo homer to left field. In the minors, Karns had excelled by limiting homers — he allowed eight to 875 batters. In the majors, four of the first 28 batters he faced went deep.

“These guys have been here for a while, and I’m new to the game,” Karns said. “This is why they’re here for a long time. They’re able to do that. They’re making it difficult for me out there. But I’m just going to continue to improve. Hopefully it turns around where it’s difficult for them instead of myself.”

The Braves put the game away once Johnson pulled Karns for Duke in the fifth. Johnson needed several innings, and he wanted a lefty to face Brian McCann. Duke, the only lefty in the Nationals’ bullpen on opening day, was allowing left-handers to hit .407 off him before the game. McCann kept the inning going with an opposite field, RBI single. Freeman, also left-handed, provided the exclamation point in the sixth inning with a two-run double off the very top of the wall.

“I’ve been leaving pitches over the middle,” Duke said. “I’m not locating sliders to them. So it makes sense.”

Following Moore’s RBI single in the second inning, the Nationals went 1 for 26 for the remainder of the game. They went quietly Sunday, still waiting to become whole again, hoping time will not have run out by the time they do.

“We’re going to hit our stride eventually,” Desmond said. “I know the fans and everyone else are getting tired of hearing that. But it’s bound to happen. We’re a good ballclub. Obviously we’re weathering this storm. Eventually, it’s going to get good and it’s going be real fun. Everyone’s going to be back out wearing their red.”