Near the beginning of the game, the NSF use Battery Park as a small base of operations for naval transport. By the time JC Denton arrives, the NSF have barricaded themselves within Castle Clinton. While the main courtyard in the castle is heavily guarded, there is also a backdoor entrance to the base. In addition, the NSF also raid the nearby subway station, taking hostages and threatening to destroy the platform with TNT.
On the second trip to Battery Park, Castle Clinton is closed up to ensure that the investigation of the base can continue unhindered. JC Denton's task is to reach the hideout of the Mole People.
Battery Park is encountered once more, where JC Denton is captured (if he wasn't already). After this, the subway entrance to Battery Park is closed for good.