第 6 季 共 26 集
播出时间：2006年7月30日
第 1 集 Future Shellshock
播出时间：2006年7月30日
With the help of Cody Jones, the future great-grandson of Casey Jones and April O'Neil, our heroes are transported 99 years into the future, where they do battle with all new enemies.
第 2 集 Obsolete
播出时间：2006年8月6日
The Turtles need parts to rebuild the time machine that brought them to the future. However Cody's shady uncle and caretaker Darrius Dun has other plans...
第 3 集 Home Invasion
播出时间：2006年8月13日
An energy based entity known as Viral escapes from her prison and seeks the technological secrets held at O'Neill Tech. There's just one thing she didn't count on : The TMNT!
第 4 集 Headlock Prime
播出时间：2006年10月1日
Leo and Raph decide to go to and see a wrestling match, but when a banned contestant - Triple Threat - crashes the tournament, Raphael decide to stop the wrestler before he goes too far.
第 5 集 Playtime's Over
播出时间：2006年10月8日
Mike has been playing his new favourite video game for three days straight. And when the sequel is announced, he is anything but calm. However Jammerhead and his thugs have their own plans for the impending release...
第 6 集 Bishop to Knight
播出时间：2006年10月15日
The Turtles are shocked to find out one of their old foes from the past is still alive and well in the year 2105. Bishop has become a top agent in Earth's government, and even though he isn't after the Turtles, they don't trust him. But Bishop offers the Turtles an ultimatum if they wish to stop crime...
第 7 集 Night of Sh'okanabo!
播出时间：2006年10月22日
After Mikey finds out Cody has never seen a horror-movie he decides to take him and his brothers to a horror-festival, only to come face to face with a real monster of horror - Sh'okanabo!
第 8 集 Clash Of The Turtle Titans
播出时间：2006年10月29日
Mike finds that in 2105 someone else has taken on the mantle of Turtle Titan. Furious, he tracks down and challenges the 'imposter'. However when Triple Threat shows up and begins to create havoc, the two costumed heroes must put aside their differences...
第 9 集 Fly Me To The Moon
播出时间：2006年11月7日
In an effort to fix the time-window Cody and The Turtles go to the moon to retrieve a special alloy, but are interrupted by The Inuwashi Gunjin - who under Darrius' instructions - are to leave none of them alive!
第 10 集 Invasion of the Body Snatcher!
播出时间：2006年11月12日
第 11 集 The Freaks Come Out At Night
播出时间：2006年11月26日
After an outing downtown, Mikey starts behaving strangely – as in super strength, green-slime-spewing strangely. The reason, the Turtles soon discover, is that Mikey has been “implanted” by one of Sh’Okanabo’s “gene-seeds”.
第 12 集 Bad Blood
播出时间：2006年12月3日
Darius Dun and Sh'Okanabo decide to join forces to get rid of the Turtles. Sh'Okanabo's new creations pose a huge threat - Enter the Dark Turtles!
第 13 集 The Journal
播出时间：2006年12月10日
While in Cody's trophy-room the Turtles find an old journal written by April and Casey. Feeling homesick they decide to read some of its content...big mistake.
第 14 集 The Gaminator
播出时间：2006年12月17日
In a effort to prove to Sh'Okanabo that she might still be useful to him, Viral sets a trap that digitises and sucks the Turtles into a prototype game system, the Gaminator.
第 15 集 Graduation Day - Class of 2105.
播出时间：2007年3月25日
Splinter announces that the Turtles will graduate to the next ninja rank, Chunin, for using the 3 pillars of life: being invisible, indestructible and showing insight. Except for Michelangelo, who skipped the exam to play video games. But Splinter gives him a last chance to graduate with his brothers.
第 16 集 Timing Is Everything
播出时间：2007年4月1日
Sh'Okanabo unleashes a time storm on New York, putting the Turtles in the middle of chaos, where foes from the past and present collide!
第 17 集 Enter The Jammerhead
播出时间：2007年4月8日
Jammerhead escapes from jail, and with the help of some new technology he has gotten his hands on, is determined to confront the Turtles. At the same time, Starlee's alien family visits Starlee on earth.
第 18 集 Milk Run
播出时间：2007年4月15日
When Torbin Zixx breaks into O'Neil Tech, the Turtles have to chase him through the city and end up on an interstellar trip. But what are his true intentions?
第 19 集 The Fall of Darius Dunn
播出时间：2007年4月22日
Dear old Uncle Darius and his evil pets have returned. Cody tries fighting Darius with his Turtle-X battle armor, but falls to Darius's superior armor. Can Cody turn the tables on his uncle, or is this the end of both him and the Turtles?
第 20 集 Turtle X-Tinction
播出时间：2007年4月28日
Turtle-X is on a rampage and it's not Cody's fault! Someone is controlling Turtle-X remotely but the question is who and why? And more importantly, will the Turtles and Cody live long enough to find out!
第 21 集 Race For Glory
播出时间：2007年9月9日
The Turtles are entering a race as Team O'Neil. Donatello modified the Hovershell to become a top notch racing machine. Also, Triple Threat is destroying everyone's cars in the race. While they are racing, the Turtles meet an ally, Falcon. Can the Turtles survive the road rage?
第 22 集 Head Of State
播出时间：2007年9月16日
An old enemy from the past returns, and he wants Bishop destroyed and only the Turtles can help him. However, when Bishop is kidnapped, the Turtles learn that before he became the Global President and cleaned up his act, he did some "dirty work" for the Earth Protection Force-- poaching and gene splicing aliens. It turns out that in 2055, there was a lab accident that had catastrophic results...
第 23 集 DNA Is Thicker Than Water
播出时间：2007年10月7日
The Dark Turtles are tired of losing and being abused by Darius Dun. With Dun’s orders to destroy the Turtles looming, Dark Leo comes up with a plan to destroy his opponents from within!
第 24 集 The Cosmic Completist
播出时间：2007年10月14日
A galactic collector who collects rare beings wants the Inuwashi Gunjin in his collection. With nowhere else to go, the Gunjin ask the Turtles for help.
第 25 集 The Day of Awakening
播出时间：2007年10月21日
Sh'Okanabo is finally ready for his last attack. The only obstacles between him and the Day of Awakening are the Turtles... aided by none other than Bishop.
第 26 集 Zixxth Sense
播出时间：2007年10月28日
Torbin Zixx was selling disintegrator weapons to aliens and cheated Big Red out of merchandise. As payback Zixx promises him an experimental matter transmitter he doesn't have - but Boss Zuko does. Meanwhile, a meteor made of dark matter is on a collision course to Earth. Can the turtles get the transmitter from Zuko and stop the meteor? Or will Zixx get there first?
