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In the Mirage continuity, the second sewer lair is the new home Hamato Splinter and his sons make for themselves after returning to New York City and killing Oroku Saki's clone in Return to New York, Book Three. It replaces the first sewer lair that was destroyed more than two years prior in volume 1 issue 2 by Baxter Stockman's Mousers. That former lair would later be given to Leatherhead to serve as his new home.

Splinter and the turtles lived in their second lair in between two separate periods of living at the Jones Farm near Northampton, Massachusetts. After the turtles return to New York (without Splinter) in City at War, Part 1 of 13, they do not return to this lair, but instead move into a water tower. What happened to their second sewer lair has never been explained in the Mirage continuity, as Leonardo and Michelangelo discover and inhabit a third sewer lair in Evolution early in volume 2.

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