Some TMNT stuff was always meant for grownups.
In the Mirage TMNT continuity, the third sewer lair is the third lair of Hamato Splinter and his sons in the New York City sewer. It replaces their second sewer lair. The first sewer lair had previously already been given to Leatherhead.
Early in volume 2, Leonardo, Michelangelo and Raphael are living secretly in the basement studio apartment of the building April O'Neil has recently bought out from Casey Jones' mother. But the conditions are crammed, and Raph becomes fed up and moves out on his own. Leo and Mikey decide to set out and find a new proper lair in the sewer, which they discover in Evolution.
This third sewer lair serves as their home for the rest of volume 2, with Splinter, Raphael and Donatello eventually moving in to live as a family once again. It remains their family lair during volume 4.
- The Mirage Comics continuity timeline establishes that a third sewer lair had to have existed, but this means the second sewer lair was abandoned for reasons never explained in any of the published Mirage TMNT comics.