The Time Twister is a time machine in the form of a large hub that can open large, orb-shaped passageways throughout time and space. Invented by Dr. N. Tropy, Uka Uka and Dr. Cortex used the machine to gather crystals from the past to be used to power the newly rebuilt Cortex Vortex.
There are five warp areas in the main level of the Time Twister, each of which has up to six warp portals to different historical areas (five normal levels and one boss level). Below the main level is a factory where Dr. Cortex manufactures robotic clones of his lab assistants and sends them into various portals through time to search for more crystals. The lower level also contains five additional warp portals that provide alternative entrances to previous levels, alongside new levels. Players can activate these portals by collecting the relics.
After the remnants of Cortex's space station destroyed Uka Uka's temple prison, he directed Dr. Cortex to use the Time Twister Machine to gather the crystals that they needed to continue their plot to take over the world, under the eyes of Dr. N. Tropy. Aku Aku, sensing his evil twin's escape, informed Crash and Coco of the threat and brought them to the Time Twister to gather the crystals first. Uka Uka and Cortex monitored their progress but made no personal intervention as they defeated Tiny Tiger in the first area and Dingodile in the second area.
Dr. N. Tropy confronted them in the third area, and upon his defeat, Dr. Cortex and Uka Uka chastised the bandicoots for putting them all in danger, as without N. Tropy looking after the machine, nobody could predict what the outcome would be.
After defeating Dr. N. Gin in the fourth area, Crash and Coco moved to the fifth area where Cortex and Uka Uka waited. Upon reaching them, the pair gloated that even though the bandicoots had defeated all of their best henchmen, they had gathered all of the crystals in the process, meaning all Uka Uka and Cortex had to do was take them.
When Crash and Coco win the final battle with all of the gems collected, Cortex's warning of the instability of the Time Twister comes to pass: the machine malfunctions and opens a massive time portal that swallows the entire machine, taking Uka Uka and the scientists with it as the bandicoots barely manage to escape. The final scene shows N. Tropy and Cortex trapped in the prehistoric past as infants and having a tug-of-war with Uka Uka's mask body, both wanting to use his power.
- The level names of "Bone Yard" and "Dino Might!" were originally the other way round in earlier builds of the game.
- Keeping with the theme of having the files for Cortex's lab assistants being named "Ass", the machine that creates the lab assistants in the sixth chamber is named "AssPress".