Reed set up their old warehouse on New York's docks as their new headquarters. While originally a warehouse like any other (outwardly it still looks like a warehouse), Reed has upgraded the building's structure and security to his exceptionally high standards.
Living quarters were quickly established. While they were riddled with Reed's technological enhancements (like the ability to fire the Fantasti-flare from any room and room-specific force fields), they have been customized by its occupant to suit his/her tastes. Franklin's room, for example, was littered with model spaceships, video games, and toys. Reed had also attached a tesseract to the living quarters and laboratories, so that they could add as much space as they need without disturbing the building's facade.
Facing the docks were three large garage doors. Office space could be accessed on the south side of the edifice. The interior warehouse space was roughly four stories high with an additional (substantially smaller) floor above that. This lent itself to both storage of a vast amount of equipment as well as Reed 's larger experiments and potentially a training center. The building's computer could be accessed by vocal commands, however only by members of the Fantastic Four. (Although some less critical functions may be activated by anyone.) All of the exterior windows depict a holographic image of an empty interior so that the Fantastic Four always maintain a high degree of privacy inside and Reed rebuilt Roberta to handle incoming calls.
In a battle between the Fantastic Four and Diablo and his elementals, Pier 4 was completely destroyed. It has been discretely rebuilt as a backup HQ.