Doctor Neo Cortex has set free a powerful entity known as Uka Uka, the mastermind of Cortex's previous schemes. He regroups with Cortex and additionally recruits Doctor Nefarious Tropy, the inventor of a device named the Time Twisting Machine which will allow Cortex's minions to collect the Crystals and Gems from their original places in time. Aku Aku leads the Bandicoots to the Time Twisting Machine, which they can use to collect the Crystals and Gems before Cortex does so.