When the Turtles' second lair was destroyed by Karai and the Foot Clan to avenge Ch'rell's exile. Leonardo was currently in Japan with the Ancient One. Leo's brothers Donatello, Michelangelo and Raphael along with their father Hamato Splinter were almost killed while trying to escape from the Foot.
When Leonardo returned and found Splinter and Donatello he had to find them a new home and soon came across the Reservoir pumping station and made it their new lair. After finding Raphael and Michelangelo the Turtles and Master Splinter try to settle into their new home.
Trying to settle in proved to be hard for the Turtles, especially for Donatello who had lost all his computer equipment, research, notes and the work he and April O'Neil had completed together. Eventually the Turtles and Splinter have their new lair properly equipped with everything they need from computers to television.
In the episode Future Shellshock!, the Turtles and Splinter are accidentally sent into the future year 2105 by Cody Jones who is the great grandson of April O'Neil and Casey Jones. When the Turtles eventually do return, Donatello with his knowledge of technology in the future upgrades his current equipment to become more advanced.
During Turtles Forever, the station came under attacked by a mutated Hun, causing the turtles and their 1987 counterparts to defend it but most of the station was damaged. It is unknown if the station was repaired after the turtles returned from their dimension travel.