The Mole People tunnels are old subway tunnels inhabited by the Mole People and taken over by the NSF during the events of Deus Ex. The tunnels are accessed by a secret tunnel in the women's bathroom of the Brooklyn Bridge Station.
The south end of the tunnels contain a secret room inhabited by the NSF commander. The children in the area allude to its existence and claim a brick behind some cardboard boxes can be pressed to reveal the room.
If the player talks to the commander he claims he's a reserve commander, previously an accountant, and doesn't want any fighting to happen. The commander tells the player that the LaGuardia Airport can be reached through the men's bathroom and points to the key on the table beside him. Upon finishing the conversation the commander tells all other NSF in the area to stand down and let the player past.
Kevin Bradley can be met on the way to the NSF commander, he can alternatively be used inside of one of the kids to get a hint on how to find the commander. The water next to him is meant to appear only if you turned on the water in the Brooklyn Bridge Station, but the logic is inversed and only appears if you didn't turn it on.
The north end of the tunnels contain the bathrooms, with the wall in the men's bathroom broken down to give access to the LaGuardia Helibase. The required key is to the north in the commander's room.
On the way to the men's bathroom north two terrorists can be heard talking about the traps in the LaGuardia Helibase tunnels, asking each other if the player has made it to them and claiming that "Paul" said not to take any chances, that he would know about the player's capabilities.