Zack Wheeler hands the ball to manager Mickey Callaway as...

Zack Wheeler hands the ball to manager Mickey Callaway as he leaves a game against the Washington Nationals during the sixth inning at Citi Field on Sunday. Credit: Jim McIsaac

Peter Alonso and Michael Conforto tried to right all that was wrong with the Mets in Sunday’s 12-9 loss to the Nationals at Citi Field. Each hit a three-run homer, but that could not compensate for what their team lacked: pitching.

The Nationals’ pitching wasn’t much better, but Washington still won the battle of the incendiary staffs.

It started in the second inning when Zack Wheeler gave up five runs, including two on a double by Adam Eaton and one on a single by pitcher Max Scherzer. That basically took the Jacob deGrom Cy Young bobblehead day crowd of 40,681 out of the game. It got way worse — 12-1 — before surprisingly getting within reach.

“Certainly disappointed we lost the game, coming up short when you put up nine runs,’’ said Conforto, whose blast off Jeff Ross in the ninth forced the Nationals to bring in closer Sean Doolittle to end the game. “It’s frustrating, 12-9 stinks, but it’s easier to swallow than 12-1. To bring it back within reach was positive. Make every at-bat count, keep moving the line. That’s the attitude we’re taking.’’

Alonso’s second homer in two games came in the five-run seventh and cut the deficit to 12-6. “We did a really good job of fighting in the later innings,’’ he said. “I’ve said this before, just us fighting back, making it a ballgame, I think that’s special characteristics in a team. We came up on the short end today, but we did a really good job.’’

Alonso is hitting .382 with three homers and 11 RBIs. “I feel really good right now,’’ he said. “I feel comfortable with my approach. I’m really happy that all my preparation is leading to success in the games.’’

Alonso, Conforto and Jeff McNeill each had two hits. Four of the runs were charged to Scherzer, who didn’t have a vintage performance, making the loss that much more frustrating.

“Scherzer doesn’t give you many opportunities,’’ Keon Broxton said. “It’s a little bittersweet. We showed that we’re not really out of any game, but it’s also kind of a downer because we did score all those runs.’’

On a day when the Nationals drew 12 walks, Wheeler took the blame for the poor day of pitching. “It was an embarrassing day for me,’’ he said. “Just one of those ones that you forget. Look forward to the next start.’’

Wheeler was charged with seven earned runs in 4 2⁄3 innings. He walked seven and left to a heavy dose of boos. Tim Peterson then walked five and allowed two runs in 1 1⁄3 innings. Luis Avilan was next and gave up three runs, two on Anthony Rendon’s homer, in one inning.

Mickey Callaway found what he called one “silver lining’’ when the struggling duo of Robert Gsellman and Seth Lugo each threw a scoreless inning. Lugo struck out the side in the ninth.

From the runs you don’t score early can cost you later department, the Mets had a freak occurrence in the second inning. Conforto hit a leadoff double and wound up on third on a throwing error by rightfielder Eaton. Wilson Ramos singled home Conforto and went to second on a hit by J.D. Davis.

After Amed Rosario struck out, Broxton came to the plate. With two strikes, Scherzer threw a high pitch that Broxton swung under before it ticked off catcher Kurt Suzuki’s glove and went behind the plate. It was ruled a swinging strike. Ramos had broken for third, where Rendon took the throw from Suzuki. Rendon spotted Davis running midway between first and second and threw to shortstop Wilmer Difo, who applied the tag for the third out.

“One of those weird baseball plays,’’ Davis said. “Fastball up or something. We were just confused. I saw Ramos take off, the back runner takes off as well.’’

Said Broxton, “I heard and felt something, so I thought I fouled it off. I didn’t foul it. I saw the replay.’’