Even after announcing his retirement as head of the MTA on the day the Second Avenue Subway opened in 2017, Tom Prendergast figured he might not be done with transit megaprojects.

“In the back of my mind, I always knew that if an opportunity availed itself, I was going to take advantage of it,” Prendergast told THE CITY Wednesday. 

Now the former MTA chief executive — who also led New York City Transit and the Long Island Rail Road during more than 20 years with North America’s largest public-transit authority — has another mammoth project on his plate as the new head of the Gateway Program, whose centerpiece is building a $16 billion rail tunnel in the Hudson River.

Prendergast was last month appointed chief executive officer of the Gateway Development Commission, the bi-state public authority whose tunnel construction project is at the heart of a network of enger rail improvements between New York Penn Station and Newark Penn Station for 200,000 daily New Jersey Transit and Amtrak riders.

After spending the last few years at AECOM, the infrastructure consulting giant, the respected transportation veteran now takes an even more daunting challenge than opening three new stations deep beneath Second Avenue.

At age 72, he’s taken the top job at Gateway to help carry out construction on what is billed as “the most urgent major infrastructure program in the country.”

“To be involved in a signature project that brings that much value is an opportunity I couldn’t up,” Prendgast said.

Five Gateway contracts have been awarded so far, including one on Predergast’s first day for  construction on the Manhattan side of the tunnel.

“It’s a massive public works project and it’s got all of the things you want in a public works project,” said Kate Slevin, executive vice president of the Regional Plan Association. “Not only is it good for the economy and job creation, but it’s also good for the environment and the quality of life here.”

It aims to build two enger rail tubes within a single tunnel in the Hudson by 2035 and eventually rehabilitate the existing pair of 115-year-old tubes that were heavily damaged by flooding during Hurricane Sandy in 2012. 

“Two out of three days of service, there is some kind of delay related to the infrastructure,” Prendergast said. “So that infrastructure needs to be upgraded and brought to a state of good repair.”

Gateway emerged after then-New Jersey Governor Chris Christie in 2010 scrapped a Hudson River rail tunnel project known as Access to the Region’s Core.

Work is underway in Hudson Yards on a segment of the new tunnel that will eventually connect with New York Penn Station. In addition, the bottom of the Hudson River is being stabilized for construction of a 1,200-foot-long concrete box which will allow two massive machines to cave out the New Jersey portion of the tunnel.

While a significant portion of the project will be done largely out of view to the public, Prendergast said residents on both sides of the Hudson need to know of the importance of the work.

“Our job is to effectively communicate in a very transparent way all the work that’s going on so people see what that money is being spent on,” he said.

A $12 billion commitment for federal funding is in place and several contracts have already been awarded for various components of The Gateway Program. Yet, questions remain over whether it could be slowed under President Donald Trump, whose first istration created some bureaucratic obstacles.

“We’ve seen in the past that these projects have bipartisan because they deliver so many benefits for everyday riders and for the regional economy,” Slevin said.

An analysis conducted last year for the Gateway Development Commission estimated that the project will create 95,000 jobs during construction — 20,000 more than estimated in a 2017 Environmental Study — and generate billions of dollars in economic activity.

Among the initial undertakings set to start in the coming months is construction on a section of the new tubes from a bulkhead in the Hudson that will connect to the Hudson Yards concrete casing, all while protecting existing utilities and sewer lines.

The technically complex project also requires staying in good graces with the White House, Congress and the governors of New York and New Jersey — and working with multiple states, cities, railroads, property owners, business leaders, the public and rail engers.

“You need to make sure that working on one goal doesn’t cause problems meeting the others,” Philip Plotch, principal researcher and senior fellow with the Eno Center for Transportation, told THE CITY. “It’s like working on a Rubik’s Cube with one hand and juggling flaming torches with the other, while walking on a tightrope surrounded by axe-throwing cannibals.”

Plotch — a former MTA planner whose 2020 book “Last Subway: The Long Wait for the Next Train in New York City,” chronicled the decades-long quest to build the Second Avenue line — said completing Gateway is critical for the entire Northeast Corridor rail line between Washington D.C. and Boston.

“New York lives and dies by its transportation system,” he said. “We’ve built an island with millions of people and millions of jobs because we have great rail service.”

Elected officials from New York and New Jersey praised Prendergast’s appointment last month, while former colleagues said he’s the right man for an enormous job.

”He’s going to be amazing at it because he understands it from every aspect — he knows transportation, he knows construction, he knows the railroads, he knows the region,” said Carmen Bianco, who Prendergast brought in as president of New York City Transit after he was named head of the MTA in 2013. 

“He’s a wonderful catch for them and he should bring them a lot of good will.”

Prendergast said the job is the right fit and that the “uniqueness” of delivering a single megaproject, instead of having to operate service while building around construction, is not lost on him.

“There was always the constant battle of like, ‘How do you deliver service and build something?’” Prendergast said. “Because one gets delivered at the expense of the other.

“The uniqueness of this one, is that’s what makes it different and the criticality of the project for the region.”