When The Turtle's second lair was destroyed by Karai and the Foot Clan in an act to avenge the Utrom Shredder's exile. Leonardo was currently at Japan with the Ancient One and his brothers Donatello, Michelangelo, Raphael along with Master Splinter were almost killed while trying to escape from the Foot.
When Leonardo returned and found Master 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 completed. Eventually the Turtles and Master Splinter have their new lair properly equipped with everything they need from computers to television.
In the episode Future Shellshock! the Turtles and Master Splinter are accidentally sent into the future in the 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.