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Initial design proposals were laid out by David Childs of Skidmore, Owings, and Merrill. In a protracted series of events typical of many large, complicated projects, plans to redevelop Penn Station have stretched further and further into the future. In July 2005, announcements were made that Childs' plan had been scrapped and a new one was unveiled. This second plan was similar to but much more modest than the original. It is the result of a collaboration between the architectural firms of James Carpenter and Hellmuth, Obata and Kassabaum (HOK). Later in 2005, Skidmore, Owings, and Merrill reacquired the project and released a third design, which is a compromise. As of June 2006, the design resembles the interior of BCE Place and does not require the demolition of part of the facade of the Farley Building.
Amtrak was to be the major tenant of the new building, leaving the old station for use by the NYC commuter rail passengers. Signs of construction appeared in November 2005, with plywood barriers installed on the sidewalks and orange nets covering main facade on 8th Avenue.
Amtrak, however, subsequently decided not to move from its present location, leaving New Jersey Transit as the Moynihan Station's anchor tenant. NJ Transit has been negotiating a 99-year lease on the Farley Post Office. In the meantime, Cablevision, owner of Madison Square Garden, considered relocation of the Garden to the west flank of the Farley Building. Such a project would lead to Vornado Realty Trust building an office complex on the current Garden site.
Redevelopment of Penn Station thus continues to languish as various design concepts are debated and altered. A revised version proposed in 2007 would reportedly add 1,000,000 ft² (90,000 m²) of retail space to the new Moynihan train station and office complex, prompting the New York Times to complain that this latest plan "could easily shortchange the public's interests in favor of the private developers…The last thing New York needs is another dreadful Pennsylvania Station that only serves developers and Madison Square Garden."
New York Assembly Speaker Sheldon Silver has called for greater integration of the project with the larger Midtown renovation plan proposed by developers and Cablevision.
A FAQ for New Jersey Transit's Trans-Hudson Express tunnel suggests that Pennsylvania Station, Moynihan Station, and a proposed rail station under 34th street will be considered to be separate entities. The proximity and connection of those entities would make the Moynihan and 34th St. Stations de facto expansions of Penn Station. Daniel Patrick Moynihan's daughter, Maura Moynihan, has stated that she considers the Farley Building and current Madison Square Garden to be potential sites for two Moynihan Stations: a Moynihan-East and a Moynihan-West.
On April 3, 2008, Madison Square Garden executives announced plans to renovate and modernize the current arena in time for the Knicks and Rangers 2011–12 seasons. This announcement came a week after they declared that they have abandoned plans to move the Garden to the Farley Post Office site. Hank J. Ratner, the vice chairman of Madison Square Garden said, “We're all for the development of Moynihan Station at the Farley building, as the project was originally conceived. We're not going to be moving."
On February 16, 2010, $83.4 million from the federal government's TIGER program was awarded to the Moynihan Station project, which together with $169 million from other sources allows the first phase of construction to be fully funded. New construction plans include two new entrances from West of Eighth Avenue through the Farley Building, doubled length and width of the West End Concourse, thirteen new "vertical access points" (escalators, elevators and stairs) to the platforms, doubled width of the 33rd Street Connector between Penn and the West End Concourse, and other critical infrastructure improvements including platform ventilation and catenary work. On July 30, 2010, the New York state government approved the plans; as a result, construction was expected to begin in October 2010, with completion of the first phase, including expansion of the west concourse, new entrances and improved ventilation scheduled for 2016. On October 18, 2010, the ceremonial groundbreaking of the first phase of the project occurred, with numerous government officials in attendance.