Ian Isberto and his girlfriend, Blossom, arrive in a forest where the peaceful planet called Aldabra, where Galapagus and the Geochelone Aerios lived in their home planet, is said to appear on the last month of every year. They arrive to find the planet tethered to a mountain by a chain and completely covered in metal and all of the Geochelone Aerios are terrified. Ian realizes this is the work of his arch-nemesis, Zcorpion, who is using the planet's unique time properties to make it his own base. Furthermore, Zcorpion has sent his apprentice named Brick, one of the Rowdyruff Boys and the rival of Ian Isberto, who kidnaps Blossom. Ian, with the help of his teammates (Dexter, Cyborg, Buttercup, and Gohan), Professor Paradox, Gwen Tennyson, Kevin Levin, Galapagus, and his allies called the Ben 10 Alliance (Ben Tennyson, Doopy, Robin, Numbuh 5, and Ling Yao), must traverse Aldabra and collect the Time Stones, seven jewels capable of altering the passage of time itself, in order to save Blossom, defeat Zcorpion and Brick, and free Aldabra and the Geochelone Aerios from Zcorpion's control.
- Ian Isberto - The 1st member and the leader of Team Isberto. He serves as the main protagonist of the mini-series.
- Dexter - The 2nd member of Team Isberto and Ian Isberto's best friend and sidekick.
- Cyborg - The 3rd member of Team Isberto and Ian Isberto's brother.
- Buttercup - The 4th member of Team Isberto and one of Ian Isberto's friends.
- Gohan - The 5th member of Team Isberto and one of Ian Isberto's friends.
- Ben Tennyson - The leader of the Ben 10 Alliance and one of Ian Isberto's friends.
- Doopy - The 2nd member of the Ben 10 Alliance.
- Robin - The 3rd member of the Ben 10 Alliance and one of Ian Isberto's friends.
- Numbuh 5 - The 4th member of the Ben 10 Alliance and one of Ian Isberto's friends.
- Ling Yao - The 5th member of the Ben 10 Alliance.
- Blossom - One of the Powerpuff Girls and Ian Isberto's girlfriend.
- Gwen Tennyson - One of Ben's team and the cousin of Ben Tennyson.
- Kevin Levin - One of Ben's team and a best friend of Ben Tennyson.
- Professor Paradox - A time traveling professor who can travel anywhere in space or time.
- Galapagus - One of his own species, the Geochelone Aerios, who lived in his home planet called Aldabra.
- Cody Webb - The leader of The Cody Webb Corps and Ian's best friend. He serves as the narrator of the mini-series and makes an appearance at the end.
- Zcorpion - Ian Isberto's arch-nemesis and the leader of the Scorpion Army. He serves as the major antagonist of the mini-series.
- Brick - One of the Rowdyruff Boys and Ian Isberto's rival. He serves as the minor antagonist of the mini-series.