The Underground was a secret organization of humans against the Orb Alliance. They were operating in custom made tunnels and sewers under New York, since the tracking disks were not operating underground.
Access to their locations could be found in the sewers below the Prospect Park. Tunnels below Abdul's Pawn Shop led near Empire States Building.
A cache was found in the Trinity Church where they could hide important items. Also, they had access to the American Museum of Natural History and at least one room at the top floor was used for their operations. A domesticated mutant monster guarded it.
The Underground, discovering that the Orbs pollute the air to weaken and control humans, decided to steal an orb ship and with that to take down the Statue of Liberty. Ships need four modules to operate, usually found in Orb robots. For this reason three of their number went to steal a repair robot from Grand Central Terminal.
They were however troubled by Phil Cook, a serial killer whose actions were made known by Underground intelligence.