Midtown TDR Ventures, which was originally led by Andrew S. Penson, purchased Grand Central in 2006 for roughly $80 million. The terminal itself was of little value, since it is under a long-term lease to the Metropolitan Transportation Authority at a relatively modest rent that decreases over time.

The investors were hoping to reap a fortune from the 1.2 million square feet of unused development rights, or air rights, above the terminal.

Several years ago, as the city sought to change the zoning around Grand Central to allow for much taller towers, Mr. Penson negotiated to sell a large block of those rights to SL Green. But the talks foundered, with each side describing the other in derogatory terms.

The de Blasio administration ultimately rezoned a strip of Vanderbilt Avenue, allowing SL Green to build a 65-story office tower in exchange for $220 million in transportation improvements. Mr. Penson and his group sued, claiming that the city’s action, which gave SL Green the air rights it needed to build, deprived his group of its property rights. Those rights, which it had purchased for $60 a square foot, were now worth $880 a square foot, Midtown TDR Ventures said.

Aside from damages, the suit sought to stop the project and the transit improvements.

Despite the legal challenge, SL Green had nearly completed demolition of four buildings on the block where 1 Vanderbilt is planned. But the suit, which could have made it difficult to pay for construction of the tower and could have scared off potential tenants, had cast a shadow over the project.