The Times story says, "Just last June, the state’s mass transit agency reached a nonbinding agreement with the company for the construction of a light rail station near its property."
NJ Transit itself owns several parcels next to the Rockefeller property. The area is near the city's northern border, next to Weehawken.
The Times cover story mainly pieces together the timeline of efforts by the Rockefeller development company to pressure Hoboken officials to support its project, following up on the mayor's allegations that Gov. Chris Christie's administration pressured her last spring. The story doesn't uncover any new potential illegalities, but does note that Gov. Jon Corzine's allies also helped pressure Hoboken for the project.
The Times story can be read here.