A historic season is turning into a frustrating one for Jacob deGrom.

The New York Mets ace was pulled from a second straight start with an arm injury, this time leaving after three perfect innings with right shoulder soreness, but the bullpen stepped up to finish a three-hitter in a 6-3 win over the Chicago Cubs on Wednesday night.

One start after being pulled from a gem against San Diego with flexor tendinitis in his right arm, deGrom went directly down the clubhouse tunnel after finishing the third against the Cubs.

“Felt good warming up, felt really good in the first and second inning, then there in the third my shoulder was sore,” deGrom said. “This is getting old. I want to be out there competing.”

DeGrom said initial tests ruled out a serious issue, but he planned to get imaging and more observation Thursday. He and manager Luis Rojas both said it was too early to know if he'd go on the injured list.

“I expect to go out there and give us depth and I haven’t done that like I expect out of myself,” deGrom said. “The bullpen’s done a great job of picking me up. But I can’t keep doing that to those guys.”

DeGrom appeared to grimace after a third-inning pitch to Eric Sogard. He threw 51 pitches, the last a 99 mph fastball to strike out pitcher Robert Stock, his seventh straight strikeout victim and eighth punch-out out of nine hitters.

He’s the first pitcher since at least 1901 with at least eight strikeouts over three perfect innings to start a game, according to STATS.

“First couple of pitches, I was like, ‘OK, maybe it’ll go away,'” deGrom said. “And it continued on every pitch throughout the inning. And that’s when I was like ‘OK maybe we’ve got to be smart.’

“Again, I keep saying it’s early, but this is frustrating coming out of games like that.”

DeGrom pitched one-hit ball over six scoreless innings against the Padres on Friday night before leaving with the flexor issue. He had an MRI the next day that revealed no damage, and he resumed his usual between-start routine. He started Wednesday on his standard four days of rest.

He also had a start pushed back in early May due to a sore right side and then exited a start against Arizona on May 9 when he aggravated the injury. He was placed on the injured list two days later.

DeGrom returned May 25 and gave up a second-inning homer to the Colorado Rockies’ Ryan McMahon. That’s the most recent run allowed by deGrom, whose 25 consecutive scoreless innings have shrunk his ERA to 0.54, the lowest mark ever by a pitcher through his first 11 starts.

DeGrom also had an RBI single in the second on Wednesday, raising his average to .423. He has six RBIs compared to four earned runs allowed this year, and he could be among the frontrunners for NL MVP if he stays healthy.

“What he’s doing is just amazing and to be on the other side of it obviously is no fun, but you’ve got to appreciate what he’s doing as a competitor — he just mowed us down,” Cubs first baseman Anthony Rizzo said. “I hope he’s all right. Even his at-bat — that’s the craziest stat of all.”

Sean Reid-Foley (2-0) relieved deGrom and earned the win after allowing one run over two innings. Rizzo ended the bid for a combined perfect game or no-hitter by homering with one out in the fourth.

Kevin Pillar opened the scoring with an RBI double off Stock (0-1) in the second and homered in the fifth. Dominic Smith hit a one-out solo homer in the third and added a run-scoring grounder in the fourth immediately after Francisco Lindor drew a bases-loaded walk.

The Cubs stranded two runners each in the fourth and sixth against Reid-Foley and Aaron Loup before collecting two hits, including Rafael Ortega’s two-run homer, off Drew Smith in the ninth. Edwin Díaz entered and retired pinch-hitter Willson Contreras on a flyout to center for his 14th save.

Stock, who was recalled from Triple-A Iowa prior to the game, allowed five runs, four hits and six walks while striking out three in his first big league start.

The Mets go for the four game sweep on Thursday

The Cubs will send RHP Kyle Hendricks (8-4, 4.46 ERA) who will look to extend his career-long winning streak to seven starts in the series finale.

The Mets will counter with RHP Marcus Stroman (6-4, 2.23 ERA) who has thrown at least six innings in seven consecutive starts, the longest stretch of his career

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