Crash Bandicoot: Mutiple Cortex is a direct sequel to Crash Bandicoot Rebirth. It focuses on the real Cortex, N. Tropy and Uka Uka who were stuck in time loop ever since Crash Bandicoot: Warped. There is a hole in the vortex that grows bigger and it allows Cortexs from alternate universes travel through. All these Cortexs escape from the hole and enter the real Cortex's universe. They soon decide that they will not only take over this universe, but the alternate universe too.
It is the same as it is in the first three Crash games, including Crah Bandicoot Rebirth too. You travel through each one of the alternate Cortex's universes and you fight each Cortex as boss at the end of them.
- Dr. Neo Cortex- The original from Warped. He destroys the android clone he created of himself who had been covering for him.
- Sherrif Cortex- A cowboy Cortex. He is less technical, but he is the fastest.
- Elemental Cortex- This Cortex fused with The Elemental Masks seen in Wrath of Cortex. He manipulates all four elements.
- Muscle Cortex- A much more musclar Cortex. He has barley any intelligence, but he has the strength of Tiny Tiger, Koala Kong and Dingodile combined. He comes from the Future universe, where technology is much more advanced, but he avoids technology.
- Illusion Cortex- A manipulating Cortex. He can enter the conscious of another's mind and if he manages to control the conscious, he can do whatever he wants to the person's mind.
- Mega Evil Cortex- From the 10th Dimension, this is a even more evil version of Cortex. He created Fake Crash Evil Crash and they are his top henchmen; the polar oppisite to our Dr. Neo Cortex's universe. He appears as a shadowy figure and the only thing's that aren't black on him are his eyes and the N on his forehead which are white.
- ???- Known as the final boss of the game, this Cortex is from the Cortex-verse, a universe created by all the other Cortexs.
- The Orginial Universe
- Cowboy Universe
- Elemental Universe
- Future Universe
- Illusion Universe
- The 10th Dimension
- The Cortex-verse