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The Newton Wolves will pull Heel-Face Turns.
While is very early in the series, it is a wild guess that we have a handful of redemptions of characters who will turn against Scarlemagne. The Newton Wolves are probably holding a grudge on Kipo, Wolf, and the gang over their defeat, meaning they will want revenge. Like Jamack, the wolves could also have a chance to have revenge on the main characters, but they could also eventually have an offer to change sides and join Kipo.
  • This Troper has also had similar thoughts to the above theory’s OP. To add onto it, the Newton Wolves are shown to greatly value knowledge, a trait which seems to be shared by Kipo herself. Both even have a shared interest of the cosmos. So perhaps it’s this shared knowledge and interest which may help them switch sides.
  • Confirmed: As the events of the last few episodes of Season 3, the Newton Wolves seem to no longer view Kipo as an enemy and seem to all be on the same side.

Jamack will eventually join Kipo and her friends against Scarlemagne.
Now that Scarlemagne knows Jamack let Kipo and her friends go, Scarlemagne will put a bounty on his head and show what happens to Mutes who oppose his laws. Besides, seeing how they are misfits like him, Jamack needs a pack.
  • Jossed: While he does become fond of Kipo and is fully willing to help her whenever their paths cross, he adamantly refuses to join the group on a permanent basis.

Kipo's mom was a leopard mute with the ability to take human form, like avatar.

Kipo had to have gotten mute powers from somewhere. I think what happened in Mullholland was that Tad used memories and thoughts, even repressed memories to create his perfect dreams. The half-mute and her mom may have been from repressed memories.

  • Jossed: Kipo's mother was a human who gained the ability to become a Mute as a side-effect of being pregnant with Kipo, and her transformation is into a monkey rather than a jaguar.

Dave played some part in the Apocalypse

Or at the very least he was there. It's mentioned several times that the world's been like this for 200 years, and in the last episode he mentions that he's 200 years old so...

  • Jossed: Dave existed after the apocalypse happened and came into the world after Mutes existed so he had no involvement in it.

    • Not quite. He may not have been at the start but he finished it off.

That giant ape is Kipo's mother.

It seemed to recognize Kipo, her song and want to show affection for her once it calmed down and tried to warn her to run, what's more her father expressed familiarity with it.

  • Confirmed: Kipo and company connect the dots in "Fun Gus: Part 2", with Lio outright confirming it in "Sympathy for the Mandrill".

Lio and Hugo used to work together.
They were trying to uncover the origin of Mutes and understand what exactly happened to the world. There was value in it for both because it might explain where the more violent mutes came from and give them some common ground between intelligent species. When they did discover it though Lio started exploring other ideas, like how it could be used to give humans equal footing. Hugo got nervous because Lio with that knowledge could theoretically undo the apocalypse turning the mutes back into animals or worse give humans all the best traits of mutes.

In a moment of poor judgement he destroyed their research but not before using the prototype improvement serum himself. Unfortunately it was geared for human DNA not Mute Mandrill and as a result while he did gain powers it caused serious psychological damage. He ran off not having the knowledge on his own to recreate what they'd made but with a growing case of megalomania that would lead to his empire under the new name Scarlamange.

  • Partially correct: Lio and Hugo did know each other, but Hugo served as one of the lab animals in a series of experiments to isolate what caused Mutes, rather than him being an equal lab partner.

Kipo isn't half Mute because of her mother, it's because of her father.
Lio is clearly a scientist with a lot of knowledge across many fields and he knew the changes would be coming to Kipo. Given the only evidence of her mother being part Mute comes from the daydreams of a mute tartigrade colony there is no reason to believe that's even close to true. Perhaps rather then the mute abilities being genetically inherited from her mother they were deliberately induced by her father.

Humans in the new world have a very hard lot being less durable and lacking specialized combat abilities. Perhaps as part of a longterm effort to make humans more hardy so they would be able to live on the surface Lio opted to do some genetic engineering on Kipo. It might not have been wholly for the purpose, he might have been correcting an existing genetic problem and simply made the choice to use that opportunity to his advantage. It might also mean Hugo was his first attempt but he made the genetic changes too fast without a chance to do repairative work if things went wrong.

Song Oak, Kipo's mom, died due to illness when Kipo was a baby. Or, at least that's what her father told Kipo to cover the truth - she never had mother. She could be result of his genetic experiment to make them mutes, so other mute tribes would not keep urge anymore. As we know, Lio and Scarlemagne/Hugo worked together, so Lio probably is aware of his mind control powers and what he's capable of. Scarlemagne could also be his previous genetic alteration project that failed. Kipo could also be his way to fight Scarlemagne in some no distant future, but unexpected events rushed things a little.

  • Jossed: While Lio was involved, and there was genetic modification, it was Kipo's mother who figured out the bulk of the science required to infuse Kipo's embryo with mutagen. The same research that resulted in Hugo was repurposed for Kipo.

Adding to the theory that Kipo's father genetically modified her, the Burrow is secretly running low on resources.
It's only known to the authority figures of the Burrow that the Burrow is running low on resources. Lio is one of the few privy to this information and knows that at some point, the Burrow humans will have to go up to the surface. He also knows that humans don't stand much of a chance on the surface, so he started research into genetically modifying humans to have mute/animal abilities. Kipo is a product of this.
  • Jossed: The Clover Burrow had nothing to do with Lio and Song's research, with their home burrow wishing to return to the surface to reclaim it rather than any need for resources. And both burrows are gone now anyway, so it's a moot point.

Kipo is a genetically modified clone of her mom and not biologically related to her dad at all.
If her dream episode is any indication, she looks exactly like her mother, save for her coloring. Lio and Kipo's mother created a clone of her, but genetically modified to have jaguar abilities so that she could better survive on the surface.
  • Jossed: Kipo was born the natural way but given the DNA of a Mega-Jaguar while Song was pregnant with her.

Kipo being part mute will prompt most Heel-Face Turns.
Being a half human and half mute means she clearly doesn't belong in either specie category. But it could be an important part of the key to convince a few Mute Packs to change their opinions of humans and join her side against Scarlemagne. As of right now, Kipo and the main characters have managed to earn allies in the Timbercats, the Umlaut Snakes, the Rats in Ratland, and the Fitness Raccoons, but perhaps if revealing that Kipo is a part mute, they could convince and encourage more packs to join their side in peace and balance between Mutes and Humans. This could also prompt some packs who work for Scarlemagne (the Newton Wolves, the other Mod Frogs besides Jamack, the Scooter Skunks, etc) to redeem and join this movement. Not only that but if Kipo's heritage and kind and loving nature prompts enough Mute Packs to redeem themselves and join her side, there could be enough to mute packs to form a cavalry big enough to help Kipo beat Scarlemagne's army by the grand series finale!
  • Partially Correct: While Kipo was indeed born with the DNA of a Mega-Mute in order to bring both Humans and Mutes closer together and her powers do indeed help her goals, it's really the kind hearted nature she has that convinces most Mutes to work with her. This especially becomes prominent in season 3.

The possibility of there being other Part-Mute humans.
Kipo is clearly new to her being part mute as they only beginning to activate and only during times of need. But what if there another human on the surface, older than 13 (maybe 15, 16, or older) with the same part mute abilities as Kipo, but perhaps a different animal. Another Part-Mute in the main group could act as another symbol of harmony between humans and mutes living together as well as one to be a mentor to Kipo to help her control her Mute abilities and learn how to use them at will, especially that Kipo will probably eventually be able to take an entire Mute form, she will need someone to teach her how to control the shapeshifting and take that form at her own will.
  • Partially correct: There is one other part-Mute human in Song Oak, but she's victim to Shapeshifter Mode Lock even after she regains her senses, leaving her unable to serve as a mentor figure.

That one Wolf Mute who Wolf befriended...
In Wolf's flashback, there was that one female wolf among the children who looked like she had bonded with Wolf and saw her as a friend. Even when it turns out that her parents and siblings wanted to eat Wolf the whole time, she didn't look so happy about eating someone whom she bonded with. It could be possible that this wolf is still out there and is still remorseful about betraying Wolf, so perhaps this one wolf will meet up with the main group, giving her an opportunity to give Wolf an overdue apology. Of course Wolf is still very scarred from the incident and won't forgive her so quickly. This could also be an important piece of Wolf's Character Development as she will have an opportunity to reconcile with her one wolf mute friend and learn to forgive.
  • Given Wolf's cloak is, by Word of God, made from her "wolf mom" it seems more likely the pups will show up looking for revenge and/or to recover their mother's remains. Forcing Wolf to confront her opinions of them.
  • Confirmed: Margot ends up meeting Wolf again and asks for her help to save her brother from Emilia. It's actually a trap but she ends up trying to stop her before it is sprung out of guilt. Unfortunately it ends up being too late and after Kipo rescues everyone, she and her brother are cured by Emilia, preventing any further attempt at redemption.

All the human-hating Mutes will be made to face that they're not so different from humans.
Scarlamagne's speech in episode 8 was about how, 200 years before the show started, humans forced animals to live in cages (at the zoo). Thus, he and all other anti-human Mutes see Scarlamagne's actions towards humans as karmic punishment for humanity's poor treatment of their ancestors.

At some point, the human haters will begin ranting to Kipo & Co. about how they and all other humans "deserve" to be slaves to Mutes. However, one of the gang (possibly Kipo), will then simply ask how enslaving humanity doesn't just show how Mutes are really no better than humans when it comes to how they treat non-Mutes. This revelation could shatter those Mutes' entire worldview, and make them question everything that they know.

In the end, this will cause those Mutes to ultimately decide that sticking to their cycle of hatred is really helping no one, and decide to ultimately make peace with humans and live with them instead of trying to rule over them.

  • Partially Correct: Season 3 is all about this. It takes a lot of convincing from Kipo and her friends, but the Mutes and Humans both realize this fact and start to begin to work and live together. Ironically Kipo comes dangerously close to falling into this same trap when Emelia leads her old human burrow friends into a raid on the Timbercats home, curing several of her Mute friends and nearly convincing her to attack them at their hideout. Fortunately, Dave of all people talks her out of this with an origin story about how doing the same thing almost prevented him from befriending Benson.

Hugo (Scarlemagne) will be on a Redemption Quest and meet the mutes Kipo had befriended.

After Hugo escapes, he goes on a journey to find redemption like Zuko from Avatar, and it will lead him to Kipo's mute friends from Jamack to Cotton and Camille to the Fitness Raccoons. They will tell stories about how she changed their lives for the better. Hugo will take the stories to heart and join Kipo on her journey.

  • Mirroring Jamack's situation from Season 1, Scarlemagne upon escaping will travel across the land, miserable and searching for a place to hide out, blaming Kipo for his loss of power. Eventually he encounters the TheaOtters, who fail to recognize him due to his current condition. He uses his old name Hugo as an alias to trick them into letting him crash with them. He shortly meets Jamack, who does recognize him, and they form a friendship over their common situations with Kipo. Hugo also gets a Good Costume Switch.
  • Confirmed: Kipo finally manages to get through to Scarlemagne in Season 3. No costume switch though.

Kipo will try to talk to Dr. Emila out of getting rid of the Mutes, but it won't work.

Basically Kipo attempts to convince Dr. Emila that Mutes and Humans can live and work together, but Dr. Emila attacks Kipo and attempts to kill her, only for Wolf to get hurt instead.

  • Confirmed: After curing Emilia of her mega-mute form, Kipo offers her a chance to change, but Emilia attempts to attack her, only for Mandu to block the attack by biting her arm.

Song will play a role in Scarlemagne's redemption
Once she returns to her human self, she will try to get through to Scarlemagne. Being a mutant herself who was likely experimented on by Dr. Emilia, she could relate to him even better than Kipo did. When Scarlemagne assumes it is too late for him to change, Song will use her predicament to convince him otherwise note . This would all kick start Scarlemagne's Redemption Quest.
  • Jossed: Kipo is the one who helps Scarlemagne reform. In fact Scarlemagne helps Song communicate with Kipo in spite of her mega monkey form to help her figure out how to save her friends from Emilia.

It will be revealed there are other humans trapped in Mute form
One in particular I think could be the case is Fun Gus. He may have once been a human child whose abandonment issues stem from being separated from his family at a young age and left with nobody to play with for possibly years.
  • Jossed: If there are any others, they are never shown on screen or confirmed to be human.

Dr. Emilia will turn out to have a Freudian Excuse on why she hates Mutes

  • Jossed

Song will learn how to control her Mute powers just as Kipo did
Her transformation into a Mega-Mute seemed to be an act of impulse to get away from Dr. Emilia and her associates. Unfortunately, she lost control and stayed this way for over a decade. Part of Season 3 will focus on Kipo and friends trying to help her change back. When this eventually does happen, she will gradually learn to adjust with help from her daughter.
  • Jossed: She spends half of season 3 in Mega Monkey form helping out in that state, but by episode 5 she is cured and returned to a complete human.

Dr. Emilia will kidnap Scarlemagne to create more mind control serum
To use on her new human allies should any of them consider a change of heart. Lio comes to the rescue, but refusing to abandon him again, he sacrifices himself to allow the mandrill to escape. After his Heel–Face Turn, he tells Kipo about her father's capture and the focus will then shift to rescuing Lio and the others in addition to stopping Dr. Emilia.

The Clover Burrow director and his daughter will be prominent characters in season 3.
At the end of season 2, the director of the Clover Burrow is standing next to a girl who resembles him and has a distinct design. Both characters will be given bigger parts in season 3.

Dr. Emilia does not have a tragic backstory explanation for hating mutes.
She simply resents humans having to live underground and not be the dominant species any more.

  • Confirmed: The only tragic part is that her father harshly raised her to believe these things, and any sympathy is rendered moot by her cruel actions.

There will be a scene where Dr. Emilia perfects the anti-mute formula and uses it on some sentient mutes.
A Newton Wolf for double horror, given that they value their intelligence so much.
  • Confirmed: One of the wolves and several other Mutes including Yumyan are cured.

The Newton Wolves will be prominent allies to Kipo and her cause in season 3.
Not only did Kipo save their lives, Dr. Emilia presents a common enemy to them. Most mutes will probably gang up to fight her, but the Newton Wolves will be especially aggressive given how much they value their intelligence. Their knowledge of science is also going to be very useful, especially if they need to create something to counteract her anti-mute formula.
  • Of course, they'll need to change sides first.
  • They probably will.
  • Confirmed: They do.

Dr. Emilia is going to infuse some of her supporters with mute DNA to use them as weapons.
Taking this even further, she captures and mutates Lio, declaring to cure him only if Kipo joins her side since she is the only one with the antidote. However, Kipo and friends somehow find another antidote (or anchor) that cures Song of her mutation and must figure out how to use it on the others.
  • Partially Correct: She does use Mega Mute DNA to try and put an end to Kipo. However, she uses it on HERSELF.

Dr. Emilia will eventually be driven to infuse herself with mute DNA
When all (or most of) her supporters have a change of heart and decide to stand with the mutes, Dr. Emilia turns herself into a mega-mute as a final attempt to stop Kipo.

  • Confirmed: In the final episode, she injects herself and turns into a mega-walrus mute.

Komodo dragon and falcon mutations will occur.
As shown in Season 2, these were among four DNA samples tested by the Oaks, along with jaguar and monkey DNA which have already been exhibited with Kipo and Song, respectively. Combining this with the two theories above, Season 3 will involve Dr. Emilia turning Lio into a falcon mega-mute and later herself into a Komodo dragon mega-mute (or vise versa; Lio becomes the dragon and Emilia the falcon).
  • Jossed: Only one person ends up mutating and that ends up being Emilia. It ends up being a Mega Walrus.

If Dr. Emilia has a freudian excuse, it will not be enough.
Even when a villain has a tragic backstory, it's meant to be a explanation of where the character is coming from! It is incorrect and misleading to use a Freudian Excuse to justify the villain's actions and instantly say you must show mercy, especially if they had crossed too many lines. So even if something tragic happened to Dr. Emilia that caused her to become the way is she now, it should not be enough to justify her inexcusable, wicked, and selfish actions against Mutes and the Heroes. Also, if she continues her villainous rebellion against the mutes (though to be fair, if it was only against Scarlemagne's Noble Court, that would be more karma and comeuppance rather then against all mutes), then the Heroes will have no choice but to kill her in the final season's climate.
  • Confirmed: While Emilia was raised by her father to believe that Mutes were creatures who stole the world from Humans, very harshly at that, any kind of sympathy she could have is lost by the fact that she REFUSES to accept that she is wrong, her cruel acts toward Mutes and humans who side with them, and the fact that she MURDERED her own brother when he suggested that humans and Mutes could live together and lied to her fellow burrow companions about it. Even after being saved by Kipo, she still tries to kill her in turn, and ends up being trapped by Fun-Gus for good.

The next villain

Before the mutation event, the Earth was about to collapse from environmental destruction.
This will add in an environmentalist message and add another layer of villainy to Dr. Emilia.
  • Unknown: We never learn what happened that changed the Earth into what it was.

Origins of the substance that caused plants and animals to mutate.
  • It was created by humans as a weapon. Spray it over enemy territory, now they have to fight off mutated plants and animals, making it harder to fight in the war. But it backfired on the creators by spreading all over the world. (whether through environmental means or human release)
  • It was created as a last ditch effort to save the planet. Make plants and animals stronger so they don't go extinct. It worked too well.
  • The mutation was an accident, possibly the result of a new pollutant.
  • Unknown: It's never revealed.

The Umlaut Snakes will be crucial in the fight against Dr. Emilia.
They're so used to loud noise that the noise weapon won't disable them.
  • Jossed: Kipo actually destroys the emitter herself while rescuing some Mutes from Emilias boat.

The Timbercats will be major characters in season 3.
  • Confirmed: The base of H.M.U.F.A is set up at the Timbercat village and Yumyan even gets a heroic sacrifice moment when he is cured helping Kipo save her friends.

The Newton Wolves will be crucial in the fight against Dr. Emilia.
With their scientific knowledge and their resources, they could potentially combat her reversal serum or other weapons.
  • But first, in order for this to happen, they must pull Heel-Face Turns and make with amends with Kipo.
  • Jossed: The wolves are merely a part of the alliance and one of them is even cured without either making much contribution.

For the next season and after that, Kipo needs to starts rallying mute packs and humans to work together
First it was Scarlemagne's army of Mutes-against-Humans, now it seems Dr. Emilia is starting an army of Humans-againest-Mutes. It's a safe bet that for the rest of the series until the final season that this is forming an intense Cycle of Revenge! Clearly the only way to stop it is Kipo and the group inspiring Mute Packs and humans to work together, not as an army, but as allies and friends supporting peace, balance, and harmony! Right now they have the Timbercats, the Umlaut Snakes, the Fitness Raccoons, Amy and Brad, Jamack, Tad Mulholland, the Chevre Sisters, Cappucino, the Thea-Otters, Roberto, Troy, Asher and Dahlia on their side and willing to support and/or fight for this cause. But in order to defeat Emilia, Scarlemagne, or any other villain who pops up next, they will need more Humans and Mutes willing to live and support each other in peace. With Scarlemagne defeated (for now), it's possible for Kipo to try to encourage Mute Packs that work (or worked for now) for him such as the Newton Wolves, the Humming Bombers, the Scooter Skunks, or any other Mute Pack that the surface does not have to be a "Mute-Eat-Mute World" and that mutes and humans together in peace is much better then fighting to enslave each other. In anyway, in order to truly end this Racism Cycle between Mutes and Humans, the heroes to form a group supporting this frontier!
  • Confirmed: Season 3 has Kipo set up H.M.U.F.A in an attempt to convince humans and Mutes to live together in the world. She and her friends succeed and the finale has everyone all living together peacefully in the future.

In order for Scarlemagne/Hugo to complete his Redemption Quest, he needs to die.
Don't dare call it cliche, this is logic! After all the horrible things he's done to the humans AND the Mutes allied with Kipo, they are not going to accept him, ever! Even though he has a Heel Realization, he's done too much to them, none of them will want him, even if Kipo insists on forgiving him! Therefore the only way to truly make up for what he's does in the previous seasons is to die. Whether it's a Heroic Sacrifice or dying while fighting Emilia's henchmen, it is the only real way he to redeem himself and show everyone he ever harmed that he truly changed.

  • Confirmed: He dies saving his "sister" Kipo from a mutated Emilia.

Or alternatively...
Some kind of genetic altercation (perhaps becoming a test subject of the anti-mute formula) will revert Scarlemagne back to his non-mute infant form, giving the Oaks a chance to Raise Him Right This Time.

Kipo will temporarily lose her mute powers.
Kipo will be exposed to something (most likely the experimental anti-mute formula) that inhibits her ability to use her jaguar mute-powers for a time. This will naturally occur at a time when having the powers would've been most useful. A side effect will cause her skin and hair to lose it's purple and pink color and become a normal skin tone and hair color.
  • Jossed: Kipo keeps her powers all the way to the end. In fact, she's the only one the cure DOESN'T work on because Emilia made it from her DNA.

Lio will be Killed Off for Real.
It would certainly make sense for him to feel responsible for all the things that have happened - Hugo's Start of Darkness, Song's mutation, Kipo getting lost, the burrow residents being captured - even if he is not necessarily the only one at fault. This underlying guilt will eventually drive him to a Heroic Sacrifice. Twisting the knife even more, it will happen sometime after Song is brought back to normal; Kipo regains one parental figure but loses another, driving her Character Development even further.
  • Jossed: Scarlemagne is the one who ends up sacrificing himself.

Kipo won't be able to reason with all of the humans.
Such as the case of Hugo/Scarlemagne, Kipo is still unable to accept that she can't win over everyone. Most of these humans do not know what is like to coexist in peace with Mutes, meaning Kipo will indeed be able to convince at least a good number of them (her friends from the burrow, Greta, etc) to pull Heel-Face Turns and join her cause. But let's be realistic, she clearly won't win them all! Emilia is clearly a Greater-Scope Villain, Zane is too cruel to be reasoned with, and it's a safe bet that the humans were slaves to Scarlemagne so long will not listen to Kipo's pleas at all! Kipo must see for herself that some of these humans ARE IN FACT "Lost Causes" who won't listen no matter how much heart she gives them and that some of them will have to be killed (mainly Emilia and Zane) in order to end this racism cycle.
  • Confirmed: Kipo is able to convince everyone in the end... except for Emilia.

In a Heroic Sacrifice, Scarlemagne will take Emilia with him.
As it has been mentioned, Scarlemagne has gone way too for a Heel–Face Turn, especially after attempting to molt everyone alive in the coliseum. So even if he does start a redemption arc, the mutes AND the humans (mostly Wolf, the humans he enslaved, the Newton Wolves, the Umlaut Snakes, the Scooter Skunks, everyone in that coliseum) are NOT going to forgive him just like that! Dr. Emilia clearly is the main mastermind behind Scarlemagne's Start of Darkness and now she's the show true villain and has now corrupted the humans to destroy the Mutes (just like they tried to enslave them). Just like Scarlemagne, it's clear that Emilia is much as villain who won't be reason with or give up at much as he didn't. So in theory during the last season, in order to redeem himself, Scarlemagne will commit a Heroic Sacrifice, but then last minute grab Emilia, taking her down with him and killing them both! This act will not only fully redeem Scarlemagne, but will also symbolically end the Mute/Human hatred cycle as both leader figures that used the racism for their personal gain will be gone.
  • Partially Correct: Scarlemagne does indeed sacrifice himself to save Kipo, but it ends up trapping Emilia in her Mega-Mute form until Kipo cures her. She still is punished by becoming Fun-Gus's new playmate though.

The Newton Wolves will come into conflict with Wolf's old pack.
Wolf packs can have territories spanning hundreds of square miles, and Wolf's former pack haven't come after her because Las Vistas is the Newton Wolves' territory, so far as wolf mutes are concerned at least. But, thanks to Kipo and friends weakening their position Wolf's pack will try to move in. Depending on how things turn out the Newton Wolves could be forced into an Enemy Mine with Kipo, or they figure out the interlopers are after one of the humans who destroyed their telescope and team up.
  • Adding onto this theory, something like this could be what starts the Redemption Arc for the Newton Wolves, AND the recoiling of Wolf and her old friend.
  • Jossed: Neither packs meet up with each other and Wolf's old friend ends up being cured by Emilia.

We will get a Benson and Dave backstory episode in Season 3.
At least one hint towards Dave's origins at the least was dropped in Season 2 (mentions he was around 200 years ago). We've gotten backstories for most of the cast already, so up next should be Benson and Dave's turns.

  • Confirmed: Dave tells the story of how he and Benson met in the episode "Requiem for a Dave".

The blonde girl in the pink jumpsuit (Hoag's daughter) will feature heavily in Season 3
Hoag's daughter had an unusually front and center position in the last episode. She has a very distinct and thought out character design, and was very specifically present for Dr. Emilia's speech, though not visible in many of the shots of it. She may either turn out to be someone who is secretly against Dr. Emilia, or Kipo's Azula.
  • Confirmed: Hoag's daughter is convinced by Kipo that they are wrong and ends up becoming their inside agent. Hoag himself isn't so easily convinced, but by the time they are invited to the Prahm Kipo set up, he soon realizes he is wrong too and even warns Kipo and her friends about Emilia's firework cure trap.

Fun Gus is Liam, or has his consciousness
After Emilia killed Liam, the spores that became Fun Gus infected his body to decompose it. The fungus absorbed Liam's personality, but only a primitive young mind, and will force Emilia to be his sister again.The show's creator thinks this is a cool idea

During the climate of the final episode, Emilia destroyed Lio and Song's antidote.
As seen in the Time Skip, the cured mutes are around but still not mutes, meaning something happened that Lio and Song could not make the antidote they were trying so hard on. It is a possibility that when Emilia transformed herself into a Mega-Mute Walrus, she stomped on their work for an antidote for her cure, thus preventing them from finishing it.

The cure isn't necessarily complete or permanent.
Emilia may have created a counter-mutagen to whatever evolved the animals, but the cure wasn't able to rewrite their genetic structure, only "resituate" it so to speak so the subjects appeared normal while still maintaining certain traits from their mutant forms. This means the cured mutes might still have some memories of their past lives, while Song has enhanced Monkey agility and senses and could possibly even learn to transform like her daughter. Meanwhile, Fun Gus finds his new "forever friend" is snarling at him with a pair of tusks...
  • Though Yumyan and Bad Billions are seen to still be cured after five years. Somehow I doubt even Emilia could survive that long with Gus.
    • Considering there’s probably no food or water in Fun Gus’ burrow, the only way Emilia can possibly be alive after the Time Skip is if Gus puppeteers her, which would actually be perfect karma since she would presumably experience the same Death of Personality she inflicted on Mutes.

Scarlemagne/Hugo's Heroic Sacrifice was in fact a Heroic Suicide
It has been argued by some that Hugo would have survived the crash or even leapt out of his vehicle with minimal injury beforehand. What really drives this home is this line of dialogue that implies he was aware of what was going to happen:
"I'm glad we were able to be a family one last time."
Hugo knew that, although the Oaks have reaccepted him into their family, there was no other way he could make up for all the harm he had done over the years as a tyrannical ruler.

Mutes and baseline humans will band together to restore civilization on Earth
  • Mutes will converge towards more humanoid shapes and sizes
  • The humans and sentient mutes will either domesticate or kill the giant, non-sentient mutes so as to get rid of a natural competitor and an obstacle to the restoration of civilization

The war between the Fanatics and Daves started over something completely different.
  • ...but both sides forgot what the initial flashpoint was. (For humans, due to the attrition of time and mortality, for the Daves... they're Daves.) At the start, it was something that felt as important as what Kipo and the gang are fighting over—maybe the humans felt threatened by the Daves' immortality. But by the time Benson comes along, both sides have so little left that the only thing they have left to fight over is a little handheld fan. And since the human faction called themselves Fanatics, it makes perfect sense in Dave's mind that it was always about a fan in the first place.

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