As early as Teenage Mutant Ninja Turtles issue 15 (Mirage, August 1988), the Turtles have been shown to share a universe with traditional superheroes. During volume 4 of the comic and the 4Kids cartoon (both which were being released around the same time), this theme was amplified tremendously. The most prominent of which was Silver Sentry, Michelangelo's favorite hero in the 2003 series. He was pretty much the TMNT version of Superman in many ways.
This figure represents Silver Sentry's incarnation in the series' final season, "Back to the Sewer". The art style had been retrofitted to become somewhat of a simplified version of Bruce Timm's art style, and thus a Justice League Superman was the perfect choice to transform into Double-S.