- Doctor Neo Cortex (Intermediate; best at acceleration)
- Doctor N. Gin (Beginner; best at turning)
- Tiny Tiger (Advanced; best at speed)
- Doctor Nefarious Tropy (Advanced; best at speed) (unlocked by beating all of his ghosts in Time Trial mode)
- Nina Cortex
Their story begins on a average night: Inside the Cortex Castle, Cortex is pacing in one room wondering how he could defeat the Bandicoots and take over the world. While Tiny was playing checkers by himself, he mentions that he could squash the Bandicoots with Cortex saying that he knows that but that Tiny has failed many times. Cortex sends Tiny to see if Doctor N. Gin needs assistance. While N. Gin is working on his race car, he tells Dingodile to pull the switch. Tiny arrives and squashes Dingodile who was behind the front door. Then, a strange bright light comes out of the window. N. Gin asked angrily and anxiously "What did you break now?" as Tiny shrugs being just as confused as he is. Cortex also notices the light. Meanwhile, part their castle gets abducted by Velo.
The trio later finds themselves in Velo's coliseum, as they noticed Crash, Crunch, and Coco on their abducted home. The two trios then start to fight, until they see a hologram of Emperor Velo the 27th. Velo claims that he has heard of the six's racing skills and wants them to race. If they refuse, Earth gets destroyed.
Upon choosing Team Cortex, Velo asks Cortex if he's willing to race. Cortex says "We'll win easily." After Team Cortex defeats the champions of all the worlds, Velo challenges Team Cortex to the Galaxy Championship, where Velo himself races against them. After Team Cortex wins, he gets so angry that he says that they cannot leave until they get all of the time relics and beat him once more.
After getting all of the time relics and beating Velo again, he causes himself to explode, revealing himself to be a small gremlin-like version of himself in a robot suit. Cortex decides to steal Velo's scepter. After Tiny gives Velo a mean look, Velo decides to give the scepter to Cortex. Cortex used the scepter to get back to Earth but the scepter breaks and they get transported to Terra. Tiny fixes the scepter and upon raising it, finds himself worshiped by the natives, aggravating Cortex to call him a buffoon.
- Tiny Tiger is the only one on the team who is neither a doctor, nor a human.
- He is also the only one on the team whose name doesn't begin with "N".
- All Team Cortex members were bosses in Crash Bandicoot 2: Cortex Strikes Back, Crash Bandicoot 3: Warped and Crash Bandicoot: The Huge Adventure.
- N. Tropy (who is unlockable) is only fought in Warped, however.
- All Team Cortex members are different in color (Cortex - Yellow, N. Gin - Sunburnt pink, Tiny - Orange, N. Tropy - Blue).
- All Team Cortex members drive red ATV bikes, meaning that their signature team color is red.
- It's unknown why N. Tropy is a member of the team, since he has become rivals with Neo. Although it could just be a mistake.