So the lore is in two branches at first, then goes into one. Let’s begin with branch 1: the Aku-Uka branch.

Thousands of years ago, on N. Sanity Island, there lived two witch doctors: Aku Aku and Uka Uka. One day, they decided to immortalize themselves by placing their spirits into one of their magical wooden masks.

As time went by, Uka Uka grew evil and sinister, even planning to conquer the world. The two brothers had a long war, and eventually, Aku Aku won and managed to seal his brother in Jaws of Darkness. He then lay in hibernation for a good amount of time, and now we get to the second branch: the Cortex branch.

Neo Cortex was born to a family of circus clowns but preferred scientific studies over entertaining others. Due to this, he was mocked by the members of the circus, and at the age of three, a group of performers tattooed an N on his forehead for nerd. One day, Cortex just couldn’t take it anymore and he decided to use his knowledge to enslave the planet’s inhabitants. He caused a freak explosion that killed his whole family, then worked for years on his plan. He hires Dr. Nitrus Brio as his assistant, and together, they make the Evolvo-Ray, a device that can zap animals up the evolutionary chain; as well as the Cortex Vortex, which would brainwash them into doing Cortex’s bidding.

Eventually, the two would set up a base on Cortex Island, which is in the same archipelago as N. Sanity Island. And this is when the two branches come together.

Uka Uka makes contact with Cortex, knowing they have a common goal, and they form an alliance. Anyway, Cortex and Brio create an army of genetically enhanced AND brainwashed animals, and the one to lead them all was Crash Bandicoot. BUT, for some STRANGE REASON, the Cortex Vortex doesn’t work on Crash, and the bandicoot escapes. Cortex’s next subject? Tawna, whom Crash just so happened to take a liking to.

Crash washes ashore on N. Sanity Beach, recollects the recent events, and is very upset about being distanced from his loved one, and awakens Aku Aku from his hibernation. Now Crash has to make it back to Cortex Castle to save his girlfriend, with Aku Aku helping Crash by scattering his magical wooden masks across the island to help him. Crash defeats Papu Papu, the chief of N. Sanity Tribe; Ripper Roo, Koala Kong and Pinstripe Potoroo, three of Cortex’s cronies. Crash sets Castle Cortex on fire while battling N. Brio, Cortex goes plummeting to the ground after Crash defeats him, and the two lovebandicoots reunite. We never see Tawna after this. Papu Papu sells the ruins of Chateau Cortex to a resort developer, and uses the proceeds to open a shopping center on the island, Ripper Roo undergoes higher education, Koala Kong moves to Hollywood, Pinstripe founds a sanitation company in Chicago, N. Brio becomes a bartender, Cortex’s fate is unknown, and peace is restored.

Until Cortex awakens in a cavern filled with crystals, and gets an idea. He hires a NEW assistant, Dr. N. Gin, gets to work on another mutant bandicoot who just so happens to be Crash’s sister, Coco (she escapes BEFORE the Vortex), and builds a new space station. He apparently needs more crystals for his master plan, so when Coco sends Crash to get an extra battery for her laptop, Cortex kidnaps Crash and sends him to get the crystals, claiming that he needs their power to stop a planetary alignment. Brio tells Crash to get the gems instead to foil Cortex’s plans. Crash goes with the crystal path, and Brio is forced to send his minions (former Cortex Commando Ripper Roo, and newcomers Komodo Bros. and Tiny Tiger). But at the end, Coco finds out that he’s gonna make a HUGE Cortex Vortex ray to brainwash Earth, Crash defeats Cortex, gets the gems, Brio destroys Cortex’s space station, and peace is restored.

Until the space station frees Uka Uka. Uka is (understandably) mad at Cortex for failing him twice, but decides to spare his life only because he had just been freed. New plan: get the crystals from different time periods using Dr. N. Tropy’s Time Twister.

Aku Aku notices Uka Uka is free and takes Crash and Coco to the time machine thing. They get the crystals, defeat Tiny (now with Cortex), defeat newcomer Dingodile, defeat N. Tropy, defeat N. Gin, defeat Cortex, defeat Uka Uka, the three bad guys are sucked into an asteroid for 22 years (enough time for Cortex and N. Tropy to age again from their recent baby transformation), peace is restored.

Until Uka Uka’s screaming rips a hole in the space-time continuum. N. Tropy and Cortex cross the rift, uncover the source of its power, and use it to open more rifts to enslave not only the planet’s inhabitants, but the MULTIVERSE’S inhabitants. Their opening of rifts awakens the Quantum Masks, who are scattered around the multiverse. One of them, Lani-Loli, is in N. Sanity Island, and a great power is emanating from N. Sanity Peak now. Aku Aku sends Crash to investigate, and Crash finds Lani-Loli AND a quantum rift. Crash, Aku Aku, Coco and Lani Loli cross the rift, defeat N. Gin, who is now a metalhead; defeat N. Brio that traitor, who ends up turning into a pterosaur; find Akano and Kupuna-Wa, and come across an alternate reality Tawna who is a pirate and therefore way cooler than you. When they defeat Cortex, however, N. Tropy double-crosses Cortex and announces his new plans with a new partner. Seeing that they have a common enemy, Cortex teams up with Crash and co. to take N. Tropy down. They find the last Quantum Mask, Ika-Ika, and make it to N. Tropy’s space station (actually it’s the space station of extraterrestrial racer Nitros Oxide). The new partner is a female N. Tropy who is from Alt Tawna’s universe, Dingodile retired from villainy to open a diner (it was destroyed), he got sucked into quantum rifts and met Alt Tawna, the gang goes to defeat N. Tropy, it is revealed that Female N. Tropy killed Alt Crash and Alt Coco, the N. Tropies are defeated, the gang goes for lunch at the Sn@xx Dimension, Cortex goes back in time to undo Crash, Crash and Coco defeat him, Past Cortex goes on to put Past Crash in the Vortex, Present Crash destroys the Cortex Vortex’s Regulator, the Cortex Vortex doesn’t work on Crash, Present Cortex is sent to the end of the universe, Dingodile reopens his diner, Cortex is enjoying the end of the universe, Crash, Coco, Aku Aku, Alt Tawna and the Quantum Masks now live together, N. Gin abandons heavy metal for smooth jazz, N. Brio is caged in Ripper Roo’s taxidermy display, Nitros Oxide becomes hooked on caffeine, Cortex’s lab assistants repurpose Cortex’s airship into a crystal shop, Dingodile franchises his diner, Alt Tawna takes up scrapbooking, Coco takes up eSports, the N. Tropies’ fates are unknown, all loose ends are tied, nice ending, peace is restored.

Until Uka Uka shows up in the end of the universe