After defeat at the hands of Crash Bandicoot in Crash Bandicoot: Warped, the UKA UKA attempts to free itself and the Neo Cortex doctors and nefarious tropy from their imprisonment in the past. His last-ditch effort tears a hole in the fabric of space and time and causes him to faint. Cortex and N. Tropy quickly escape, abandoning UKA UKA, and discover that the loophole they use links their universe to the rest of the multiverse and decide to use it to conquer all dimensions. To ensure success, the pair create a generator capable of opening other space rifts and enlist the help of doctors N. Gin and Nitrus Brio to provide an army in anticipation of interference from their enemies. Meanwhile, Aku Aku, UKA UKA’s older twin brother, senses the disturbance in space and time and quickly rushes to N. Sanity Peak. Upon arriving, he comes across Lani-Loli, whom Aku Aku recognizes as one of the Quantum Masks—four ancient sorceress masks who have great power over space and time and who would only appear if something opened up the multiverse. Lani sees a breach and suspects there is trouble, leading to Crash and his sister Coco agreeing to follow him through the multiverse and find the other Quantum Masks, while combating the chaos cortex he is creating.
During their adventures, the duo meets an alternative version of Tawna, Crash’s old girlfriend, who offers help while undertaking an adventure of her own. At the same time, Dingodile, who recently retired from villainy to run his own restaurant, finds himself caught in the chaos when his business is burned down by a rival restaurant and he is sucked into another dimension by a space disaster. Although Dingodile does not interact with Crash’s adventure at first, his actions inadvertently help Crash and Coco at various points in space and time. Crash and Coco find two more quantum masks, named Akano and Kupuna-Wa, and defeat N. Gin and N. Brio. After confronting and defeating Cortex, N. Tropy betrays him and reveals that he and his new partner (later revealed to be an alternate version of N. Tropy from Tawna’s universe) will remake the multiverse and subsequently erase Cortex, Crash. , Coco and the masks of existence. An angry Cortex agrees to team up with the bandicoots and the three rescue the last quantum mask, Ika-ika, and eventually meet up with Dingodile and Tawna. Together, the team successfully tracks down and defeats the two N. Tropys and the quantum masks destroy the rift generator, sealing all disruptions in spacetime.
However, after making a celebratory trip to a futuristic city, Cortex betrays the group and steals Kupuna-wa, using her to travel back in time before the events of his first attempt at world domination, in an attempt to prevent the creation of Crash. Ultimately, he is unsuccessful in convincing his past self to abandon the experiment and kill the present accident, Coco and Aku Aku, who followed him from the future. As the quantum masks banish him to the end of the universe, the past cortex proceeds with the experiment, preparing to brainwash the past with the cortex vortex; The present accident accidentally destroys the vortex’s power source, causing it to function and fail to brainwash his past, thus ensuring his own creation. Dingodile rebuilds and reopens his diner, Cortex relaxes on the beach and enjoys peace and quiet, and Crash, Coco, Tawna, Aku Aku, and the Quantum Masks play video games in their home on N. Sanity Island. After an epilogue narrated by Crash detailing the fate and whereabouts of the game’s characters, Cortex’s relaxation is interrupted by the sudden appearance of Uka Uka.
