Donna and the Doctor find a laboratory beneath the Thames and then the secret Racnoss lair is revealed in 2006 Christmas special "The Runaway Bride".
Source: The Doctor Who Locations Guide
The Judoon search for their quarry throughout the hospital in episode 3x01 "Smith and Jones".
UNIT investigates the ATMOS factory in episode 4x04 "The Sontaran Stratagem". From episode 4x05 "The Poison Sky".