The Metropolitan Transportation Authority may soon have the option to buy Grand Central Terminal, but the building’s air rights could stand in the way.

The clock starts ticking in 2017. The agency will then have two years to decide whether or not it wants to buy the terminal, as well as tracks along the Harlem and Hudson lines, according to the agency’s net lease on the property.

A spokesperson for the MTA told The Real Deal that the agency “intends to assess the opportunity as it arises.” However, the investment group that owns the terminal — Midtown TDR Ventures — has the option to delay this purchase another 15 years if it doesn’t sell at least 1 million square feet of Grand Central’s 1.2 million square feet of air rights by the time said “opportunity” arises.

The city’s Midtown East rezoning proposal could complicate any air rights deal. Though it would allow owners of air rights to sell them to other sites throughout the district — the current zoning rules only allow transfers to adjacent properties — it’s unclear how it would impact the demand and price of the air rights.

The proposal gives landlords two options to build or redevelop office buildings that exceed current zoning regulations: They can buy some of the 3.5 million square feet of unused air rights from landmarked properties in the area, or they can pay for specific transit and infrastructure improvements. The city is currently studying what these specific improvements would be.

About 2.3 million square feet of these air rights are owned by sites such as St. Patrick’s Cathedral, Central Synagogue and St. Bartholomew’s Episcopal Church, and landlords could turn to those sites before tapping into Grand Central. Plus, an unspecified percentage of the air rights sale — based on square footage — would go to the city’s “improvement fund” for public improvements in the area.

Robert Shapiro, president of City Center Real Estate , which specializes in assemblage and air rights, said the sudden flood of air rights on the market could devalue the price of the rights to between $100 to $200 per square foot.

“Whoever can make the quickest, easiest deal will sell first,” he said.

The city is currently assessing how much the air rights are worth. Joseph Zwilling, director of communications for the Archdiocese of New York, which owns St. Patrick’s Cathedral, is hopeful the city will value the air rights at a price that will benefit owners even after the city takes its cut. He also said oversaturation of air rights was not a sure thing.

“I don’t think it’s necessarily a given that everyone will rush to market with the air rights,” he said. “I think we would more realistically be looking at a development of air rights over a good number of years.”

A representative for the Department of City Planning said the Midtown East proposal is still in it early stages and would not speculate on how it might impact Grand Central’s air rights.

How much the terminal’s air rights are worth has been a contentious topic for some time. Then-owner Andrew Penson of Argent Ventures sued the city and SL Green Realty last year, alleging that his air rights were rendered worthless by the “Vanderbilt Corridor” rezoning, which enabled SL Green to move forward with plans for its office skyscraper, One Vanderbilt. That lawsuit was settled for an undisclosed amount in August, shortly after Michael Dell’s MSD Capital bought a stake in the terminal for $63 million . It’s not clear what role, if any, Penson currently plays in the investment group that owns the terminal and its air rights, though SL Green touted the terminal’s new ownership as the reason the parties were able to resolve the lawsuit. Representatives for Penson did not return multiple requests seeking comment.

A spokesperson for Midtown TDR Ventures would not comment on the air rights beyond saying that the group “is working with the city to ensure the best outcome for all stakeholders in the rezoning of East Midtown.”

In its rezoning proposal, the city identified 16 sites ripe for redevelopment, owned by landlords such as RFR Realty, SL Green, RXR Realty, Argent Ventures and Solil Management. Together, the sites currently have a total of 6.9 million square feet of office space, and would be able to add another 6.5 million square feet under the new zoning rules. City officials hope the rezoning pushes developers to spruce up the area’s aging building stock.