In the opening scene where Cortex, Tropy and Uka are stranded at the beginning of time, there is a rock with twenty-two tally marks on it. It has been 22 years between Warped (1998) and its direct sequel It's About Time (2020). It has also been that long the three have been stuck there.
The T-Rex that chases Crash in the prehistoric levels notably does not swallow and eat Crash if it managed to catch the poor bandicoot, unlike damn near everything else there. Notice when it starts chasing you, its surrounded by chicks and eggs! It's going to take Crash to its offspring and feed him to them!
Fridge Horror, you just orphaned a bunch of baby dinosaurs by escaping it.
Why do Nitro Crates appear in the Flashback Tapes and Cortex Castle while absent in the first game? Cortex needed more R&D time before rolling them out.
It seems odd that despite being a villain, Cortex is actually the least lethal of the playable characters — he can't kill enemies by jumping on them, and his only attack turns them into platforms. But then, being turned into a platform is not only a Fate Worse than Death (especially if it can't wear off without Cortex zapping them again), it also forces them to act as his stepping stone or trampoline against their will. Cortex's gameplay isn't about killing enemies, but forcing them into unwilling servitude — which goes in-character with his M.O. of brainwashing others into serving him.
It might seem like a bit of a plot-hole that Kupuna-Wa, the all-seeing Quantum Mask of Time, apparently did not foresee Cortex’s betrayal at the end of the game. That is until you remember she sees every moment in time, which would also include seeing Crash and Coco follow Cortex into the past, ultimately foil his plans, and maintain the timeline. In other words: she knew Cortex would inevitably abuse her power to go back in time, but she did nothing to stop it because she already knew everything would work out fine in the end. Furthermore, she had to let it happen so present-day Crash would wind up causing the Cortex Vortex to malfunction and reject his past self, thus completing the time-loop that is revealed to be Crash’s origin.
There's also the fact that, while she can see every moment in time, that doesn't mean that she can see it all at the same time. Or that she remembers it all.
You might wonder why, if Uka-Uka can brute force a way out of a space-time prison, why he didn't just do that before the series begins. It's more than likely he tried, and was so exhausted afterwards his brother could just toss him back inside. Smashing a hole in space-time took so much out of Uka-Uka that he was rendered unconscious-he probably didn't bother freeing himself without any backup because Aku-Aku could sense this and then re-seal him later.
As discussed by this tweet, Crash's actions in the second game are recontextualized through how this game fleshes out his relationship with Cortex. Dialogue from the Flashback Tapes reveals that Cortex viewed Crash as like a son to him before his escape, and the main game shows that Crash still views Cortex as a father figure to some degree, happily hugging him when they decide to team up. Thus, Crash's reasoning for helping Cortex collect the crystals in Cortex Strikes Back was less due to utter stupidity and more because Crash genuinely hoped that there was some good hidden in his creator. A Horrible Judge of Character regardless, but it makes sense from his perspective. The same also applies to N. Brio.
This game's time-and-space multiverse doesn't just provide insight into how Crash came to be, but the teaser for its reveal allows the player to infer the exact fork in the timestream that leads to It's About Time as opposed to The Wrath of Cortex. Unlike Cortex Strikes Back, Warped has two completely different endings as opposed to endings that imply a second final confrontation. Wrath happens if you don't get 105% completion, as it leaves Uka Uka and Cortex able to escape and recoup their losses over the course of three years. If you do collect everything, then It's About Time happens, sending them into time rift and leaving them there for twenty-two years.
That's false, actually. Not only did supplementary material for The Wrath of Cortex referenced Cortex, Uka Uka and N. Tropy being sent to their prison in time, but the endings from Warped were never intended to be separate outcomes. Warped is designed so that the player (via normal means, anyways) has to go through the normal ending first before reaching the 105% ending, due to how levels become inaccessible immediately after an area is completed until their boss is defeated, and how Relics (and replays for each level) are needed to collect all the Gems. Story-wise, the normal ending has Cortex and Uka Uka escape specifically to collect the Gems later as they "still have a chance to triumph". When fighting the final boss again after getting all the Gems, the boss intro cutscene changes to Uka Uka referencing how Crash now has all the Gems, and in the 105% ending, enough time has passed for the Time Twister to collapse in on itself and throw Cortex, Uka Uka and N. Tropy into the time rift. Both endings of Warped are canon to each other in the same way that Cortex Strikes Back's were.
With the game being so difficult, you're likely to see quite a few death animations for every character. Which should also tick you off that Dingodile's heroic turn is genuine when he's an angel and Cortex's is not when he's a devil.
Tawna mentions a "Shnurgle shank" on the restaurant planet, implying that the adorable little alien mount on Bermugula in the Crash Landed level is on this planet's menu!
Since Dr. Nitrus Brio was last seen captured in the Taxidermy exhibit, it's safe to say that he's been Killed Off for Real. Even more scathing, he was killed and stuffed by Ripper Roo, one of his own creations! Talk about a horrifying (if fitting) way to go...
Cortex seems to be okay with being banished to the end of the universe at the end of the game, but look around — it's a totally barren wasteland. Was Cortex so desperate and weary of the fight that he was content to die out there alone of thirst/exposure/starvation? That is, until Uka Uka shows up alive and well, probably ready to punish him for the abandonment or drag him kicking and screaming back into the cycle of villainy he'd been trying to escape. Either way, it's A Fate Worse Than Death and a lose-lose situation for Cortex.
Kupuna-Wa offhandedly mentions a "giant, mask-eating monster from beyond the stars", which possibly dwarfs the power of everyone else in the franchise. Best hope that nobody ever encounters it...
The Reveal in the intro — after being turned into babies, Cortex and N. Tropy actually had to grow up in the prehistoric times and wait for Uka Uka to make a dimensional rift. Imagine being turned into an infant and having to grow up again, now in a dangerous time period, all while your only guardian is the guy who was your Bad Boss. Is it any wonder that Cortex is on the verge of a Despair Event Horizon and N. Tropy goes completely off the rails with his plan to reset the universe?
Uka Uka was left behind in the prehistoric times. At the end of the game, the Quantum Masks banish Cortex to the end of the universe. And yet, Uka Uka meets him there. Did Uka Uka just revitalize? If not, when did he reawaken? What if he's the reason the end of the universe is the way it is?
Alternatively... what if he took The Slow Path back? Remained there until the end of time, forced to sit there to recuperate as the world ended around him without even being the one to cause it? And what if having to experience billions and billions of years of isolation has now given him a new spark of inspiration?
In Dingodile's first level 'Home Cookin', the main enemies are a clan of mutated bats, and the intro cutscene for the level implies they have been violent business rivals for quite sometime. Said cutscene also mentioned one item for Dingo's Diner, Bat Tacos! Which begs the question, has Dingodile been feeding his customers the corpses of his enemies? Are the bats really attacking Dingodile just to get rid of a rival business or is it an act of vengeance? Either way, it does bring to question whether everyone's favorite pyromanic hybrid truly has changed his ways.
The later Flashback tapes show Cortex just selected another bandicoot from his subjects to experiment on after Crash (that being Coco) and she ended up escaping a year later. This would imply that Crash rescued Tawna and only Tawna during his return and left the other captives, his own sister included, to their fate, with likely a few casualties after Cortex Castle set on fire. No wonder Coco is more contemptuous of Crash in this timeline.
Adding to that, while N Sane Trilogy amped up Coco's abilities, her and Crash were still equals and kindred spirits. In It's About Time, their direct sequel, there's a clear shift in balance, Coco has grown out of a lot of her flaws and Crash has seemingly gotten even more incompetent, with his allies visibly less patient and close to him. In this timeline, Crash might regress and Coco might surpass to the point the former is totally obsolete, if not something worse (true, this sort of happened in the original timeline as well, but it was universe-scale, so no one "grew out of" Crash).
It adds extra Fridge Horror to the Flanderization in the previous timeline as well. In those games, Crash didn't become obsolete, but he did become more and more animalistic, while Coco started off similarly very lucid and intellectual only to become more and more bumbling and absent minded. Several other mutants also become more deranged and dim-witted (besides Tiny, ironically). Looked at one way, it almost comes off like Cortex's experiments are unstable and slowly decay in intellect as time goes on.
In another Adaptation Personality Change example, N Tropy was evil in the original timeline, but still pretty much a petty egotist like all the other scientists (to the point that in Wrath of Cortex, he shows similar jadedness as them about going after Crash over and over), while here he is much more vicious, sinister, and The Unfettered to an extreme, betraying all his comrades and Uka Uka with the intent of "wiping it all clean". It is easy to imply that something during his banishment that didn't happen in the old timeline left him in a reallynasty mood.
Notice when the T-Rex starts chasing you, its surrounded by chicks and eggs. The level ends with you escaping the Rex, while the dinosaur dies in lava. You just orphaned a bunch of baby dinosaurs. Also, it's probably a good thing that Crash, Coco and the Mask's left the Eggipus Dimension, otherwise they would had faced vengeance driven mate of the dead T-Rex, since scientist now believe that Tyrannosaurus was monogamous.
, Crash's actions in the second game are recontextualized through how this game fleshes out his relationship with Cortex. Dialogue from the Flashback Tapes reveals that Cortex viewed Crash as like a son to him before his escape, and the main game shows that Crash still views Cortex as a father figure to some degree, happily hugging him when they decide to team up. Thus, Crash's reasoning for helping Cortex collect the crystals in Cortex Strikes Back was less due to utter stupidity and more because Crash genuinely hoped that there was some good hidden in his creator. A Horrible Judge of Character regardless, but it makes sense from his perspective. The same also applies to N. Brio.