Sean Manaea of the Mets looks on after Game 5...

Sean Manaea of the Mets looks on after Game 5 of the NLCS against the Los Angeles Dodgers at Citi Field on Oct. 18. Credit: Jim McIsaac

Sean Manaea didn’t want to leave New York and the Mets didn’t want to see him go.

After a season of reinvention in Flushing, one in which he went from reclamation project to staff ace, Manaea and the Mets decided to run it back. They agreed to a three-year, $75 million contract pending a physical, a source confirmed on Monday.

Manaea, who will turn 33 on Feb. 1, also reposted a series of Instagram stories heralding his return, as did free agent Jose Iglesias. Manaea’s contract includes a 10-year, $23.25 million deferral, according to a report in The Athletic.

The Mets brought in Manaea on a two-year contract last offseason after he pitched to a 4.44 ERA with the Giants in 2023. The second year of that deal, though, came with a player option worth $14 million that Manaea rejected, given his performance last season.

The lefthander went 12-6 with a 3.47 ERA and 184 strikeouts in 181  2⁄3 innings. He also filled the gaping rotation hole left by Kodai Senga’s absence and helped lead the Mets to the NLCS, where they fell to the eventual World Series champion Dodgers.

Manaea had a 2.70 ERA in July — a pivotal month in which the Mets began their playoff push in earnest. At the end of that month, motivated by watching Atlanta lefthander Chris Sale pitch, Manaea decided to experiment with a lower arm slot. The move paid off: Hitters had a hard time picking up his pitches and he was getting more swings and misses.

“Let me try this,” Manaea told Newsday last season. “I feel like naturally, I want to get lower and lower and lower, but for the longest time, it was like, we’ve got to climb higher ... So that was like an internal battle where I should be having a higher arm slot but naturally I want to get down lower, so when Sale pitched against us, it was like, ‘OK, this guy throws from a super-low angle; why shouldn’t I try that?’

“I tried it the next day. It felt good. The sounds it made, the feeling it made in different body parts, it just naturally feels really good.”

All of it was part of a sustained effort to improve after he struggled with San Diego and San Francisco. He began working with the Driveline Baseball pitching lab after a tough 2022 with the Padres in which he had a 4.96 ERA in 158 innings. He introduced a sweeper to his arsenal and started throwing harder.

Last season, he openly said he enjoyed his time in Flushing and would like to return.

“I definitely had a lot of crazy expectations — ‘It’s tough to play in New York; if you do bad, it’s not going to be a fun time,’ ” he said. “But I was like, maybe I’ve just got to lean into this, and if we want to be great, then let’s go take on a hard challenge. I think it’s been kind of like that.”

Manaea joins a rotation that (for now) features Senga, former Yankees reliever Clay Holmes, David Peterson, Frankie Montas and Paul Blackburn.

Manaea’s signing comes amid a busy offseason for the Mets, who inked Juan Soto to a record-setting 15-year, $765 million contract and beefed up their rotation by signing Montas and Holmes, who will attempt to transition from the bullpen to the starting rotation.

“We continue to have resources in Steve and Alex [Cohen, who own the Mets],” president of baseball operations David Stearns said earlier this month when asked if the Soto megadeal would hinder further spending. “They continue to support us in very robust ways. Where we spend those resources remains to be seen and how far we go remains to be seen. But throughout their time here, Steve and Alex have supported the baseball initiatives to the fullest extent.”