For several months, 4kids' website featured a "Director's Cut" of the movie which contained eight minutes of footage that were cut from the TV broadcast, and eventually Paramount's 2010 DVD as well. Among the scenes restored:
- The Turtles using sonar to search for the Technodrome underground
- Karai explaining that she found the Technodrome when her monitoring systems revealed that Ch'rell had changed location
- Karai claiming the Technodrome for the Foot Clan
- Splinter settling an argument between the 1988 and 2003 Turtles
- Casey and April fighting robotic Foot Ninjas
- Leonardo detailing Shredder's scheme to the Mirage Turtles
- Shredder nearly disintegrating himself and Karai (among others) while strangling the Mirage Turtles
- Various gags and one-liners
