NEW YORK -- In a major setback that puts the rest of his season -- not to mention the rest of his Mets tenure -- in jeopardy, rehabbing pitcher Noah Syndergaard was shut down from throwing for the next six weeks. Assuming at least a month-long ramp-up once he restarts his throwing program, Syndergaard will not come off the injured list until August at the earliest.

“We pray that he can pitch for us this year,” Mets manager Luis Rojas said.

Although Syndergaard did avoid the worst, learning this week that an MRI exam revealed no structural damage in his right elbow, there is enough inflammation in the joint that the Mets believe shutting him down is the correct course of action. Syndergaard, who felt discomfort in his elbow during a Minor League rehab start on Tuesday, has not pitched in a big league game since undergoing Tommy John surgery in March 2020.

“As tough as it is for us to hear, I can’t imagine how tough it is for him,” Rojas said. “This guy works really hard. He was in unbelievable shape. He was throwing the ball like you expect him to throw the ball, with all the force that he has, and probably that caused this to happen.”

Syndergaard made his rehab debut last week with a four-inning outing for Low-A St. Lucie, where he hit 97 mph on the radar gun. The Mets had scheduled him for another four-inning stint on Tuesday, followed by a progression that would have him continue to increase his innings count before joining the Mets in mid-June. But Syndergaard instead lasted merely 16 pitches in his second start.

According to multiple people on site in Port St. Lucie, Fla., Syndergaard’s velocity dipped from the mid-90s to mid-80s during that inning. But Rojas downplayed the severity of Syndergaard’s setback late Tuesday evening, terming his issue “more like a discomfort” than “soreness,” before MRI results revealed the updated diagnosis.

Syndergaard will work with Mets physical trainers on eliminating the inflammation from his elbow so that he can restart a throwing program in August. Once he does that, Syndergaard will need to follow the usual progression before returning: playing catch off flat ground, followed by bullpen sessions, live batting practice sessions, simulated games and, finally, Minor League rehab games. For most injured pitchers, that process takes four to six weeks, which would bring the 28-year-old Syndergaard well into August. Any subsequent setbacks could end his ability to return before becoming a free agent in November.

Rojas would not commit to a timeline for Syndergaard beyond the six-week shutdown, even while calling the current issue “big.”

“We were just counting on him being here a month or less than a month from now, and this happening is tough,” Rojas said, referring to Syndergaard’s original mid-June return target. “All in all, it’s good to hear that there's no structural damage in the UCL, but let’s see. … I think this is the right approach, being preventative.”

The Mets are at least growing healthier elsewhere in their rotation. Jacob deGrom (right side tightness) returned from the injured list on Tuesday, and Taijuan Walker (left side tightness) could do the same as soon as Friday against the Braves. For now, the Mets will roll with those two, Marcus Stroman, David Peterson and Joey Lucchesi. One other starter, Carlos Carrasco, has yet to debut this season due to a right hamstring tear suffered in Spring Training. He is also going through a slow rehab progression and won’t join the Mets until at least late June or early July.

In the interim, the Mets have no plans to stretch out Seth Lugo, who is due back from the injured list next week, as a starting pitcher. The Mets have been reliant on several relievers capable of throwing up to three innings at a time, including Sean Reid-Foley and Robert Gsellman. Lugo will join that group when he returns from right elbow surgery.

Other than that, the Mets are running thin on starting depth options. Tenth-ranked prospect Thomas Szapucki, who owns a 2.77 ERA at Triple-A Syracuse, could debut at some point this summer.

The Mets will hope for Syndergaard’s eventual return as well, even if it’s only for a few starts down the stretch. Although the recovery from Tommy John surgery can be routine for many pitchers, a significant number do have issues coming back from the operation. Most notably in recent years, former Mets pitcher Zack Wheeler needed more than two years to return, struggling to find success until 3 1/2 years post-surgery.

Syndergaard has offered no public updates on his Tommy John recovery, declining dozens of interview requests over the past 14 months and granting his only recent interview with GQ magazine, where he spoke about his book club and daily wellness routine.

Overall, Syndergaard is 47-30 with a 3.31 ERA over five seasons with the Mets. He is making $9.7 million in his final year of team control, and he is one of 17 players on the Mets’ injured list.

“It can be hard not to have some of the guys healthy and around,” Rojas said. “You want to see them here, and they want to be here, competing. But as hard as that is, you always want to take into consideration that everything has its time.”