Darius is eventually presented with the Dark Turtles, ferocious clones of the Turtles created by Sh'Okanabo as minions, in return for the blueprints to the Time Window. However, it becomes apparent that a combination of sunlight and Earth's oxygen-based atmosphere is preventing the Kanabo symbiosis from occurring. Other enemies the Turtles must contend with are the Kanabo warlord Sh'Okanabo and his sentient computer virus ally Viral, who seek to unleash the 'Day of Awakening' on Earth. Aiding Darius is the Inuwashi Gunjin, avian-themed warriors from an endangered species that are initially enslaved by Darius before being freed by the Turtles. As the Turtles and Splinter try to help Cody make a time portal for them to return to the 21st Century, they must uncover the suspicious criminal activities being carried out by Cody's greedy uncle Darius Dun. Due to the multispecies population of New New York City, the Turtles can openly move about and interact with everyday people. Having suddenly transported 100 years into the future, the Turtles and Splinter arrive in the year 2105, where they befriend Cody Jones, heir to a vast tech company O'Neil Tech and the great-grandson of April O'Neil and Casey Jones, and his fussy yet loyal English-accented robotic servant Serling. Volume 1, named 'TMNT Fast Forward: Future Shellshock!,” was released on February 6, 2007, and had the first thirteen episodes, and volume 2, named 'TMNT Fast Forward: Day of the Awakening,” was released on August 7, 2007, and had the remaining thirteen episodes. The episodes were released in partial season sets. Chronologically this season comes after the 'Ninja Tribunal' season. Thus mass confusion has ensued regarding which season is officially season five and which is season six.

4Kids Entertainment later signed a deal with Comcast and this season began airing on Comcast-On-Demand in August 2006. After the scheduling change was made, Mirage and its partners decided to finish production on the 'Ninja Tribunal' episodes and release them directly to DVD. This season became the fifth season to air on commercial television even though it was the sixth season produced.

The season was originally going to air one year later, but to try to increase interest in the series, FOX's 4Kids TV started airing this season a year earlier instead of the 'Ninja Tribunal' arc. The season is lighter in tone and less violent than previous ones, with a greater emphasis on jokes, and includes recreated designs for all returning characters.

The sixth season (subtitled Fast Forward or Teenage Mutant Ninja Turtles: Fast Forward) originally aired between Jand October 27, 2007, beginning with the 'Future Shellshock' episode.

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