 In the early 1990s , New York governor Mario Cuomo allocated $ 22 million to renew planning and design efforts for the Second Avenue line , but in 1993 the MTA , facing budget cuts , removed these funds from its capital budget . In 1995 , the MTA began its Manhattan East Side Alternatives ( MESA ) study , seeking ways to alleviate overcrowding on the Lexington Avenue Line and improve mobility on Manhattan 's East Side . The study analyzed several alternatives , such as improvements to the Lexington Avenue Line to increase capacity , enhanced bus service with dedicated lanes , and light rail or ferry service on the East Side . The favored alternative , build alternative 1 included a subway running down Second Avenue , from 125th Street in Harlem to the existing Lexington Avenue – 63rd Street station with provisions for expansion to the Bronx and to Lower Manhattan . Build alternative two would involve the addition of a separate light rail service between Union Square and Broad Street that would serve the Lower East Side and Lower Manhattan . Due in part to strong public support , the MTA committed in 2000 to building a full @-@ length subway line along the East Side , from East Harlem to Lower Manhattan . In 2001 , a contract for subway design was awarded to DMJM Harris / Arup Joint Venture . 
