Mother Nature was the only thing that could stop Noah Syndergaard Thursday night at Citi Field. The Indians certainly weren’t going to.

Syndergaard was in the midst of a dominating performance — a two-hit shutout — when the skies opened in the bottom of the sixth inning. Wild wind and pouring rain chased the players off the field and the fans from the stands, forcing a 2-hour, 28-minute rain delay that ended what could have been a magical night for Syndergaard.

The big right-hander allowed both hits in the top of the sixth inning. He retired the first 16 batters he faced, protecting a 2-0 lead the Mets had earned on a two-run double by Wilson Ramos in the fourth. The game was eventually called after rain stopped the game again in the eighth, allowing Syndergaard (9-6, 3.71 ERA) to collect the well-earned victory.

“When you have to stop the game when he’s going so good you say, ‘Oh no,’ ” Mets manager Mickey Callaway said. “He threw a heck of a game.”

Syndergaard may have thrown his best pitch long after he left the mound. He might have been motivated by a pregame tweet from the Indians’ team account that called the Mets “a fringe post-season team.” After the Mets were declared a 2-0 winner, Syndergaard tweeted: “We got some FRINGE for you right here, we call it a SWEEP in NYC. #LFGM”

The weather was an unwelcome and sudden intrusion in the wave of momentum the Mets were riding before and during the game. They were not only trying to sweep a three-game series, but also claim their fifth straight win and 13th in their last 14 at Citi Field.

Syndergaard was certainly up for the task and deserved to finish what he started. Displaying a wicked fastball and baffling changeup, he owned the Indians from the start of the game when he struck out the first two hitters he faced.

Syndergaard didn’t give up a hit until his 60th pitch of the game. That’s when Cleveland’s Tyler Naquin slapped a low liner into center field that Juan Lagares caught on one bounce. The crowd, which was just starting to sense a perfect game might be possible, immediately gave Syndergaard a standing ovation saluting his effort.

Syndergaard hardly flinched, continuing his dominating performance that was helped by a couple of spectacular defensive plays. Left fielder J.D. Davis made a brilliant over-the-shoulder catch at the outfield wall to rob Greg Allen of an extra-base hit in the fourth inning. And in the sixth, first baseman Pete Alonso dove to his left to snag a hard ground ball and then tossed it to Syndergaard to rob Allen of another hit. Allen, twice burned, wasn’t a happy camper as he slammed his helmet in disgust, while Syndergaard and Alfonso celebrated by bumping chests.

“I need to work on that a little bit,” Syndergaard admitted.

At that point it looked like he was headed for a complete game, something the Mets needed after exhausting their bullpen in a 10-inning, 4-3 win on Wednesday night. But after Michael Conforto laced a two-out base hit to right field, Citi Field turned into a monsoon as the grounds crew raced to cover the infield and fans scurried for safety.

Syndergaard’s premature finish left him having allowed just the two hits over six innings. He had five strikeouts and no walks over 73 pitches. It was a solid bounce-back performance after taking a hard-luck loss in Kansas City on Aug. 16, when he surrendered two runs on five hits. It was also the eighth straight start that Syndergaard had worked at least six innings.

A second rain delay in the eighth inning proved only more frustrating, prompting Syndergaard to tweet: “Figure it out, Game is Over.” Finally, it was called, giving Syndergaard the victory.

It felt like a special night from the outset. Too bad we’ll never know how special it could have been.