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It was a big moment for a big rookie. The Mets were down two runs in the bottom of the ninth with runners on second and third and rookie catcher Francisco Alvarez at the plate facing San Diego Padres closer Josh Hader.

It was a favorable matchup for the 21-year-old Alvarez, the Mets’ top organizational prospect and a power-hitting catcher known for crushing left-handed pitching. But the comeback fell short when Alvarez swung through a high cutter for strike three to end the game.

He had been looking for a fastball.

The Mets fell 4-2 on Tuesday night at Citi Field, evening the series at 1-1.

“He’s got good pitches,” Alvarez said through a translator.

The focus of this game will be on Alvarez and his 0-for-3 performance because he’s one of the top prospects in baseball. Some of the attention is warranted. But the blame lies on a lineup that failed to capitalize on runners in scoring position.

“It’s a lineup. It’s a lot more than Francisco,” manager Buck Showalter said. “There were a lot of things that happened in that game that could have gone differently, but I understand why people want to focus on that.”

Down just 2-1 in the top of the ninth against the San Diego Padres, the Mets were still within striking distance. Even after Dennis Santana gave up a two-run homer to Xander Bogaerts, the Mets came back in the bottom of the frame, threatening to walk it off.

The Mets cut the deficit to two runs in the bottom of the ninth when Tommy Pham laced a single up the center to score Pete Alonso and advance Jeff McNeil to third base. But the theme of the game was the Mets’ inability to drive in runs and the ninth-inning theatrics came to an end with a loss.

It was a dismal offensive showing for the Mets, who managed only five hits and went 1-for-8 with runners in scoring position. They had the bases loaded in the first inning with none out and failed to capitalize.

“A good pitcher made some good pitches,” Showalter said of left-hander Ryan Weather. “He had good stuff tonight and we knew he was going to be a challenge. I thought [David] Peterson was the key to us being in that game. He really pitched well, he attacked and it was good to see him get after it tonight the way that he can.”

Making his third start of the season, Peterson (0-2) set himself up for success with good counts and good command through the first four innings. Other than a two-run double to Manny Machado, Peterson was effective, limiting the Padres to two earned runs on six hits, walking two and striking out six over 5 2/3 innings.

Peterson had high praise for Alvarez as a backstop, building on the relationship they formed last season with Triple-A Syracuse. Showalter wanted to highlight the positives and Peterson was happy to help.

“From the first time I threw to him until now, there have definitely been improvements,” Peterson said. “He wants to be a good catcher. Everybody sees the offense that he’s put up, but he really takes pride in the catching position.”

Weathers (1-0), the son of former Mets and Yankees right-hander David Weathers, gave up back-to-back singles to Francisco Lindor and Alonso with none out, with Lindor getting to third on Alonso’s hit. Alonso was then picked off at first for the first out in the inning but a fly ball by Mark Canha scored Lindor to make it 1-0.

Weathers earned his first win of the season in five innings of work. It was the fourth time the Mets lost when facing a left-handed starter (2-4 overall).

The Mets threatened in the eighth when Eduardo Escobar drew a leadoff walk. He was replaced by pinch-runner Tim Locastro, who stole second base. But Alvarez then struck out on three straight sliders from right-hander Steven Wilson.

Making his second start at catcher in place of the injured Omar Narvaez, the Mets liked the matchup against the left-handed Weathers, but Alvarez went 0-for-2 against him before Wilson and Hader struck him out.

Brandon Nimmo walked and Starling Marte grounded into a force to put two on with two out, but Wilson got Lindor to swing through strike three to end the inning and the threat.

“Some good things happened,” Showalter said. “Locastro continues to make an impact on the bases for us, Tommy Pham had a big hit for us off a tough pitcher. There are some at-bats that fell to people other than Francisco Alvarez.”

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