After the Fantastic Four and other costumed heroes were presumed dead in the wake of their battle with Onslaught, Four Freedoms Plaza was stripped clean of all the FF's equipment by Vernard and Reed Richards' father Nathaniel, who sent it into the Negative Zone to keep it out of the hands of the United States military.
Upon their return, the Fantastic Four could not move back into Four Freedoms Plaza, as it had been destroyed by the Thunderbolts, shortly after the revelation that they were actually the Avengers' longtime foes, the Masters of Evil. Thus, the Fantastic Four moved into a retrofitted warehouse along the Hudson River which they named Pier 4. The warehouse was destroyed during a battle with Diablo, after which the team received a new Baxter Building, courtesy of Reed's former professor Noah Baxter. This Baxter Building was constructed in Earth's orbit and teleported into the vacant lot formerly occupied by the original Baxter Building and Four Freedoms Plaza.