NEW YORK -- In what has become a far too familiar scene at Citi Field, Jacob deGrom walked off the mound in the third inning on Wednesday and proceeded directly down the clubhouse tunnel, kicking the base of the wall in frustration. deGrom had just thrown three more perfect innings to reduce his Major League-leading ERA to 0.54. But he departed with a sore right shoulder, leaving the Mets in search of answers.

“I don’t even know what to say,” deGrom said. “I’m pretty aggravated with it.”

With that, the story of deGrom’s 2021 season -- for better and for worse -- continued on an otherwise idyllic night in Queens. As usual, deGrom was unhittable, striking out eight of the nine batters he faced in a 6-3 win over the Cubs. Dominic Smith and Kevin Pillar homered. Six relievers provided plenty of support.

But a cloud hung over those proceedings as the Mets and their fans fretted over baseball’s best pitcher. deGrom had exited his previous start after only 80 pitches due to what the team called a bout of right flexor tendinitis, but he completed his between-starts routine without issue and convinced the Mets that he was fine to pitch on Wednesday. To that end, his first and second innings appeared normal. But as he warmed up for the third, deGrom felt discomfort in his shoulder, noticeably shaking his arm after a pitch to Eric Sogard. When the discomfort did not dissipate, deGrom made the decision to cut short his outing.

“That’s what’s really frustrating about it -- you take the mound feeling good,” he said. “Tonight, the first two innings, I felt probably the best I’ve felt all year. Had good command of everything. Was able to throw the ball to both sides of the plate, and then go out there in the third and this pops up.”

Initial strength tests revealed no hint of a major injury, but deGrom will undergo an MRI on Thursday to make sure that’s the case. Even if it is, the Mets may look to be cautious with their ace, who has already dealt with various ailments this year -- back stiffness, right lat soreness, right side tightness, right flexor tendinitis and now right shoulder soreness. Asked if those issues could all be interrelated, deGrom said he doubted it. But the Mets could still take the decision out of his hands, potentially placing him on the injured list out of an abundance of caution.

That’s something they didn’t do five days ago, after deGrom experienced his flexor tendinitis. Asked if he regretted the decision, Mets manager Luis Rojas replied: “No, no, not at all.”

“Everyone was on board,” Rojas said, citing all the Mets doctors, trainers, coaches and front-office staffers involved in the decision. “Even though he exited last game, there was no feedback that would give us a red flag that he shouldn’t. … I can’t regret this, just because everyone was on board with Jake going tonight, especially Jake.”

Initial feedback indicated not a re-injury, but a new worry for deGrom, who hasn’t dealt with a documented shoulder injury since his rookie season in August 2014. That issue cost deGrom only two starts, and he was back at full strength by the end of the month.

Since then, deGrom has developed into one of the game’s best and most durable pitchers in the Majors, eclipsing 200 innings every year from 2017-19. He has also become baseball’s hardest-throwing starting pitcher, topping out at 102 mph and frequently hitting triple digits.

“He creates so much force,” Rojas said earlier Wednesday. “I don’t know if it’s something that is causing him some of the tension in some areas at times. But what I can tell you is his mechanics are so clean. They’re fun to watch, and his anatomy for a pitcher is perfect -- the long extremities and everything, it’s beautiful to watch.”

As he often does, deGrom hit 101 mph against the Cubs, adding to his legend with a run-scoring single for his sixth RBI of the season in the second. He threw 10 triple-digit pitches on the night, upping his season total to 138 -- 129 more than any other Major League starter. Like Rojas, deGrom tends to refer to his clean mechanics when asked about his velocity potentially contributing to injuries. But the two-time Cy Young Award winner sounded less confident than usual following Wednesday’s start.

“I don’t know the answer to that,” deGrom said. “It’s frustrating. I don’t know where to place the blame, whether it’s [my velocity] or I don’t know where it came from, honestly.”

For now, he and the Mets will wait for more hard medical information. Team officials understand that no one is more important to their success than deGrom, who has pitched to a 1.91 ERA over the past four seasons. They also know they have the luxury of time, if they choose to use it. Wednesday’s victory moved the Mets to 10 games over .500, matching their high-water mark over the previous four seasons.

“We’ve been dealing with this all year,” Pillar said. “As much as we look forward to every fifth day and watching Jake out there [trying] to do something historic every single night, we just rely on the next guy. … We’re built for this and we’re battle-tested, and we showed it tonight.”