After returning to New York City, Splinter and the turtles established a second sewer lair. It was around this time they first met Leatherhead, and let him live in the original sewer lair they had long since abandoned. This second lair features in the main comic series only in volume 1's Leatherhead, Too, but is featured in many other backup stories and various Tales of the TMNT stories set during this time period. Splinter and the turtles eventually left this lair for unknown reasons, returning to the farm for a period of time before City at War.
In City at War, Splinter, April and Casey went their separate ways, the farm was boarded up, and the turtles returned to New York City. For the first half of City at War, the turtles were squatting inside an abandoned empty water tower above the rooftop of a building. This lair was eventually destroyed by Karai in an attempt to forcibly flush out the turtles so she could talk to them.
In volume 2's Memories of the Future, Splinter and Donatello lived together in the wilderness as the turtle was recovering from the traumatic injuries he sustained in City at War.
In Evolution, Raph moved into the belfry of a cathedral, while Leo and Mikey found a third sewer lair to live in. The belfry was never shown again, and Splinter, Raph and Donnie were living in the third sewer lair after volume 2 ended. This lair would continue to be their home during volume 4.