After the events of Mind Over Mutant and the failure of the NV's Modern Cortex escaped the destruction of his space head which plummeted towards Earth. Failing to defeat Crash Bandicoot Modern Cortex teamed up with Modern Doctor Nefarious Trophy and utilized N. Trophys time travel technology to travel back in time and team up with his past self Classic Doctor Neo Cortex.
Both Modern and Classic Cortex would hatch what would be there greatest scheme ever and with assistance from Modern and Classic N. Trophy they used a vortex to kidnap both Modern and Classic Crash and there family and friends to a hyperspace warp room in outer space.
In Crash Bandicoot Past and Future Modern Cortex and Classic Cortex stayed behind the shadows but appeared occasionally to battle there time period Crash Bandicoot at several points in time. Modern Cortex would use the Doominator against Modern Crash but gradually towards the end both Modern and Classic Cortex destroyed the universe with a total event collapse knowing both Modern and Classic Crash were winning and with both Modern and Classic N. Trophy defeated there plan was put into jeopardy. Modern and Classic Cortex piloted a giant Cortexbot in the dead universe to battle against Modern and Classic Crash but were defeated and the universe was restored.
Modern Cortex and Classic Cortex ended up as prisoners of time again outside the universe itself having never existed and by any means could not escape and started to argue. The time prison around both Cortex's however would not seal them forever and eventually the time prison broke down and this allowed both Modern and Classic Cortex to escape and part ways and return to there own times.