Generator Rex/WMG

Generator Rex takes place in the Metal Gear universe, or a variation of

 * Doctor Holliday is Naomi, she uses nanites to artificially preserve her life, and keep her youthful.
 * Providence is a finger of the Patriots
 * Six is a clone of Gray Fox in a successful attempt to replicate the perfect soldier projects without the deaths of subjects or expenses of memory wipes.
 * The event was not an accident, it was purposefully staged to bring the war economy closer to non-conflict areas. It was also an attempt to create an organic Metal Gear, because the costs of making one is more than merely growing one.
 * Each Evo is an experimental organic Metal Gear, the designs for each of them are distributed randomly through SOP
 * Van Kleiss is perhaps Vamp, motivated by the loss of his Dead Cell comrades, he has a similar goal to Big Boss towards creating a nation for soldiers.
 * More to come
 * Fun theories. But I think that's more like Fan Wank than something that would actually be true.
 * But really, can't the same be said for just about any WMG?

The Sonic Universe is actually a future version of the Generator Rex Universe
Which is why there are talking animals with special powers everywhere. They're EVOs.
 * Robotnik is the last remnant of Providence trying to wipe out EVOs.

Van Kleiss is...
The head researcher of the nanite event. It keys into his whole "nano-messiah" vibe, he called the head researcher "The Wisest of them all" and him being caught at ground zero of the explosions explains his dramatic(but limited) powers, as well as why he gets a sovereign nation; no country wants a nanite-infested pile of dirt.
 * ...and/or Rex's dad Put here solely because Van Kleiss said Rex was there when the Nanite Event happened.
 * Alternately, Van Kleiss is Rex's Creepy Uncle because, seriously, the sequence where Van Kleiss's multiple robo-tentacles pierce Rex's stomach and drain him of nanites while Rex screams in pain was the rapiest example of cartoon techno-vampirism ever.
 * All Jossed. He wasn't the head researcher or Rex's dad, though the uncle thing is still open.
 * Rex's older brother. In "Dark Passage", Dr. Rylander tells Rex he has a brother, and that Rex's powers protected them both from the Nanite Event.
 * Strangely enough, they both have red eyes, black hair, and sort of similar skin tones. could be a taller, gaunter Rex if you think about it.
 * Jossed.
 * Alternately, Van Kleiss is Circe's father. Look at their hair and their eyes. They're the exact same!
 * ''Or, perhaps, Breach's father". It goes along with the theory about the Pack belong. Plus, they both have pale skin and long black hair.
 * Or...

Van Kleiss is Rex's excess nanites.
Take a look at Rex's Phlebotinum Overload in the Batman Cold Open of "Frostbite". The nanite tumors are trying to connect themselves to the ground. Up until Rex joined Providence and they started siphoning off the extra nanites every month or so, Rex would Walk the Earth curing EVOs until he hit capacity, then put down roots somewhere and turn it into a mini-Abyssus. His amnesia-striken body would struggle free and wander away to continue the cycle before his mind, infused into the dirt, could figure out how to control everything. There may be other Van Kleisseseses out there, or the one we've seen so far may make it a point to track down his "brothers" and assimilate them. As to why Van Kleiss is the Big Bad while the current iteration of Rex is a hero, Amnesiac Dissonance seems to be canon, at least between the current Rex and the one that hung out with the street rats in "Rabble".
 * Jossed. He was a minor lab tech before Rex ever got nanites.
 * Zak Saturday grown up. Zak got turned into Van Kleiss of Generator Rex by the Nanite Event.
 * Currently actually just a back up copy left in Abyssal. His real self is still in limbo in South America.
 * Not Zak Saturday, but Zak Monday. The nanites brought him back from the dead, and reconstructed him to look more like Zak Saturday. Zak and the other Secret Scientists got stuck in Kiev and went EVO, or they would already have a cure for the nanites.

Van Kleiss was affiliated with The Pack, pre-Nanite Explosion.
He's "eaten" every other nanite infested being that's worked with him before but keeps those three around. With Circe, he's just keeping her around to get close to Rex. With the other three, possibly related/previous work affiliates?
 * Maybe Biowulf and Skalamander were a couple of the other scientists.
 * This does seem to be the case, given how he acted in episode 9. Whether he was part of the project or one of the people funding it, is yet to be seen.
 * Even more likely, now that Caesar has revealed more backstory. There were three scientists who wanted to weaponize the nanites back before The Accident, who were always left in shadow- probably them.
 * If Van Kleiss is to believed,
 * Biowulf and Skalamander are Rex and Cesar's parents. Which is which is hard to tell at this point, but it is amusing to think of Biowulf being Mrs. Salazar with the lack of anything maternal in 'Wulf's manner. Of course they'd be amnesiac from their mutations since Biowulf.

Rex is...
A formerly dangerous and/or evil EVO. Rex refers to himself as "So secret, they have to keep me locked up", and White Knight hints at unsavory alternatives if they don't keep him under control. Rex doesn't seem to realize it, but this implies that Providence knows more about Rex than they're telling. Perhaps Rex went on a rampage, and Providence captured him. Through experimentation, they discovered Rex's healing abilities, then wiped his memory so he'd be more cooperative when they trained him to be a Tyke Bomb.
 * As of "Promises, Promises", the "formerly dangerous and evil EVO" part has been confirmed. His Superpowered Evil Humongous Mecha Side fell apart after one battle with Providence, and amnesia-stricken Rex stumbled out of the debris.
 * Alternately/Relatedly: Rex is a Tyke Bomb creation of Van Kleiss and or Providence, the unwitting Patient Zero and trigger of the nanite event, and possibly even Van Kleiss's biological son. Combining a bunch of the above and below theories: Van Kleiss was a scientist with Providence or it's direct rival. He injected a specially chosen or genetically engineered child, either his clone or biological son, with the nanites, as part of an experiment. Things either went horribly wrong, or horribly right, and now Providence may be using their own progeny to set right what once went wrong.
 * This may tie into Rex's name. If he was the first viable host/growth medium for replicatable nanites, his designation might've been Generator X.
 * Maybe Generators IX, VIII, VII, and so on are out there somewhere
 * Jossed. He predates Providence, and Van Kleiss was evidently a nobody before the accident.
 * But does he predate the Nanite Experiment? The Age Gap between Rex and Cesar seems large, if Cesar can just pop out of the timestream for 5 years and still come back older than Rex.
 * A mutant. His ability to control machines isn't the result of his nanites, its a genetic mutation that allows him to control them. That's why his nanite constructs break down when his emotions do, even though other EVOs don't seem to have that problem.
 * Rex might not be an EVO, his nanites could still be dormant, he is just controlling them with his powers.
 * Alternatively, Rex and Van Kleiss, or rather, the real Rex and Van Kleiss were both killed during the event, and reanimated by the nanites. Rex was already infected before the event, and Van Kleiss somehow caused the event, which exposed him to the version 2 nanites. Most of Rex's brain and body were fried, and so the "nanite Rex" can only recall a few residual memories of the original. Considering what happened to a character with a similar powerset to Rex's...
 * Rex is a creation of the scientists he considers his parents and Cesar. In that way, they really are his parents.

Eventually, Rex will..
...be able to transform into a full-on Humongous Mecha. He's already got the giant hands and feet, plus he absorbs even more nanites from all the Evo monsters he beats. And, of course, it would be awesome!
 * Confirmed! Seen in a flashback in "Promises, Promises". However, it seems to be a Super-Powered Evil Side, possibly brought about by untreated Phlebotinum Overload. If it happens again, it will likely NOT be awesome.
 * Related Theory: Rex will be able to Mega Man. He absorbs Nanites, so it's probably going to happen at some point.
 * Possibly leading to the above Humongous Mecha guess?
 * Jossed, at least for now. Stated directly, in the preview for episode 6, in which he can't take on any more nanites, or he'll suffer some sort of catastrophic overload.
 * Whose to say he won't try to overcome this? His abilities and obvious critical ties to the "Event" make him probably the most powerful being on earth, so it's very well posssible he'll hone his absorbing abilities to do even greater feats.
 * Rex has now; probably some new programs/powers in there.
 * Related Theory: Rex will be able to to create new EVOs by reversing the polarity of his "shutting them down" power.
 * Jossed

Agent Six's parents died in the Nanite Explosion.
That's why he's so distant.
 * Alternately, his wife died in the Nanite Event.
 * He just ''doesn't like to talk about it (the past).
 * Or...

Agent Six will soon turn into an incredibly powerful EVO,
Forcing Rex to kill him. It would make a good season finale.

Agent Six started wearing suits when started going out on missions with Rex
So Providence didn't seem so violent or war-mongering

Sometime in Season 2, a true EVO Civil Rights group will make itself known

 * A real Zombie Advocate Type. Not the weird version Van Kleiss is trying to pass himself off as.
 * They will demand that the Bug Jar be opened.
 * Or No-Face from the Bug Jar got out and is actually leading them.
 * Semi-Comfirmed:
 * The Bug Jar was wiped out by Alpha in the Crossover episode with Ben 10.

Circe's powers are what attracts Rex to her.
It just so happens that Circe likes him back.
 * Van Kleiss will use this to turn Rex against Circe, especially post the events of Alliance.

Circe will become another Big Bad.
Her powers will eventually let her control EVOs, and she'll be a bigger threat than Van Kleiss because Rex likes her, and she's not tied down to any specific locale.

White Knight is...

 * The primary backer/corporate supervisor of the research that lead to the Nanite Explosion. If he's not an astronaut, he must have known or been paranoid enough about the work the scientists under him were doing to be Crazy Prepared for a worst case scenario that, in fact, came to pass.
 * The very first person Rex cured. I have no idea how this could work, but it'd add a certain layer to their dynamic.
 * Partly confirmed. He's not the first, but Rex is responsible for White Knight losing his nanites.

ZAG-RS will return.

 * It's headed to find someone who it knows hates Rex: Van Kleiss. Eventually, though, it will try again to destroy all nanites worldwide, forcing Rex and Van Kleiss to work together to stop it.
 * How's Rex supposed to warn Providence about ZAG-RS without revealing the secret of the Hidden Engineer Village?
 * What if ZAG-RS contacts White Knight? And tells him it can destroy all nanites, without mentioning the "it will kill every living thing on Earth" part?
 * Worse, what if ZAG-RS busts out and contacts Hunter Cain? He doesn't even believe that Nanites are in everything.
 * Rex made the point that he would expose the village for the good of the planet.
 * And ZAG-RS is an evil AI; what's to stop it from lying, or at least witholding parts of the truth?
 * This is confirmed to have happened in the episode Gravity. Of course it's unknown if Rex was successful this time in stopping the crazed AI or not.

ZAG-RS was originally a Providence Project
It got discontinued when it developed a mind of its own.
 * That's why White didn't sound too surprised to hear that something like it existed.
 * Who else could have made it?
 * As it turns out,

Breach has a crush on Rex.

 * She was crazy and delusional enough to believe that once she showed Rex her dollhouse, he'd fall in love with her and gladly be her boyfriend/plaything. For no reason other then this WMG makes the episode "Breach" that much creepier.
 * Also, one of the reasons she acted independently (other then the fact that Van Kleiss would most likely disapprove) was because she was jealous of Circe and wanted to piss her off. (The next sentence is spoilered to protect tropers from the possible need for Brain Bleach.)
 * (The next sentence, while spoilered to avoid spoiling the previous entry, will hopefully remove aforementioned need for Brain Bleach.)
 * Four arms, two of which are giant, would certainly make for an interesting time.
 * ...ow, I just got Mood Whiplash.

The old guy in the first episode was taking a shower.

 * Think about it. He's the only EVO so far to not have Magic Pants; other than possibly being a nudist, which isn't too likely in such an urban area, there are very few reasons to be naked in the middle of the day. Ergo, he may have been showering when his nanites went nutso.

Rex is wearing the same outfit as he was five years ago in the hopes that someone will recognize him
Because, come on, even Six changes outfits every five years.

Six is blind.

 * Hence his Sunglasses At Night, but he has a few active Nanites that enhance his other senses to the point that it doesn't matter.
 * That's a rather interesing theory. Though we'll have to wait and see if he indeed has a reason for hiding his eyes. It's possible he's got a Cyclops thing going on.
 * If he's blind, he's not compensating with nanite powers, since it's been proven that he's not an EVO. He may just be a Handicapped Badass though.
 * Or, maybe he's blind and his sunglasses are a high-tech device that lets him see!
 * Jossed. He takes his sunglasses off in Divide by Six. They're perfectly normal sunglasses, and he has perfectly normal eyes.
 * This makes him more badass than he was before.

The School in "Breach" is actually an insane asylum...where Breach grew up.

 * In the early parts of the episode when Rex is asking Holiday where the hell he is, Breach said "its a school...but its not a school...but its a school". Now, one would think she's referring to the school being her creepy psycho dollhouse, but when it shown the whole town is in her pocket dimension, it doesn't really make sense. And why Greenville, Ohio, out of every place in the U.S. (other than the fact that Ohio is just plain freaky). The realization for this troper came when he remembered how in one work of media there was a quote of someone saying "they sent me away to schools, and hospitals disguised as schools", etc. Its possibly that Breach was already looney before she got infected with nanites (think about it tropers, it is possible for any criminal or serial killer in the world to "pop" in the world of Generator Rex), sent to the Boarding School of Horrors which was actually an juvenile insane asylum (Hey, is there a trope for that, because I've Seen It a Million Times). When she got her powers, Bleach took the entire town because it was the closest thing to "home" she's ever had.

The injection...

 * ...Contains a blueprint of the original, stable nanites and all of Dr. Rylander's research. Hence that infuriatingly cryptic comment about "Everything". As Rex gets more attuned with his nanites, he'll be able to read it -- and then he'll know everything. Or at least Rylander's take on it.
 * ...Is a treatment for Rex's recurring amnesia. Either to prevent it from happening again or to restore all of his memories.
 * Will convert all nanites Rex come in contact with into his stable variant. Note how Rylander was obsessed not with eliminating the nanites, but with fixing them. Presumably there's a trigger of some sort; either a place, a phrase, or a certain concentration of nanites absorbed by Rex.

Rex's Brother...

 * ...Will be the next big bad after Van Kleiss is taken care of . Possible rage of jealousy of his brother being pumped full of "good" nanites?
 * It will most likely be either someone we already know in the story, or else someone introduced as an independant character before The Reveal. Shows love this kind of drama.
 * Maybe Rex's brother is Van Kleiss.
 * Or Noah. Contradicts some WMG's on this page, but adds to other ones. It's an idea...
 * OR Rex's brother is Circe afterall the nano changes could manifest in all sorts of ways, not to mention how amusing Rex's reaction would be. don't look at me that way this is WILD mass guessing
 * Or Biowulf.
 * All Jossed. The brother, Caesar, was one of the scientists, previously absent from the setting due to relativistic time dilation of his fast-moving lab-escape pod, and is a kooky-but-kind positive figure.
 * Really? He struck me more as a Cloudcuckoolander with a bit of a ruthless streak, and very protective of Rex.
 * Actually, it isn't jossed just yet. Caesar might just end up being the next Big Bad...

Rylander is Noah's father.
They look quite similar. In Dark Passage we are told that Rylander had *a wife and a young son, but after it was proved the son wasn't Rex, this was never brought up. It would also explain why Noah is so desperate to win the war: he wants to erase his father's mistakes.
 * Wouldn't White Knight have done some sort of background check?
 * Maybe that's part of the deal. Noah wants to forget about the whole thing, and he asked White Knight to lie about his identity. In return, he would befriend Rex.
 * I think we can joss this theory, as episode 11 Operation: Wingman showed Noah in what appears to be his own house, and nothing seems to suggest he's alone.
 * If I remember correct, he could still be living with his mom. So it's still a possible theory.
 * Plus, his concern for a scholarship (in "Rampage") implies financial problems, which seems more like a problem for a household with only one income generator than two.

Rylander is Rex's father.

 * His exact words were: "I'm not who you want me to be", that is not the same as "I'm not your father", in fact almost sounds like he is running away out of guilt. And it's completely possible that he was lying to Rex when he said he didn't know about his dad.
 * Somewhat supported by the fact that he he named Rex.
 * Maybe Rex and his brother were homeless kids. That's why Rylander got to name Rex, and why he became Patient Zero, because who's going to miss a couple of sick, homeless children?
 * Jossed by Caesar, Rex's brother.

Dr. Holiday's sister likes being an EVO.

 * Alright, lets review the facts, shall we. Rex can cure any EVO that wants to be cured. If an EVO does not want to be cured, then it can block Rex. If Dr. Holiday's sister had become so far gone that she had lost her mind, it would make sense for Rex to be able to cure her. But if Dr. Holiday's sister still had enough of her mind left, and for some reason liked being an EVO (This troper has no idea why, maybe she's on the borderline between sane and off the deep end or something. Though it was kind of odd how smart Holiday's sister was as a supposedly non-sapient EVO, and how she didn't harm any of her victims). Because she doesn't want to be cured, Rex can't cure her, and because she can't talk, they have no way of telling that she wants to be that way, and so would think she was 'incurable'.
 * Jossed

All EVOs retain their original personalities

 * The Pack and Rex aren't anomalies because they stay in control, they're anomalies because their transformations don't hurt. Most of the EVOs of the week are in painful transformations that cloud their entire sense of reason.
 * Or, remember how Rex couldn't control himself when he overloaded with nanites? Maybe The 'insane' EVOs just had too many nanites activate all at once.
 * Meaning the key isn't how smart you are, or how strong your personality is, just how many nanites activated.
 * Does that mean that, if Rex took away just enough Nanites, they would be like Skalamander and Biowolf?

Rylander and Van Kleiss were converted into more Nanites.
The generator was a nanite conversion chamber, which converts any matter inserted into the doorway.
 * A really interesting way to bring Van Kleiss back would be to have those Nanites fly over Abysus and reform him.
 * That be pretty neat, and certainly would make killing him harder if it became a new ability of his.

Agent Six is Nigel Uno.

 * Both of them are the stoic Only Sane Man of their teams, have number-based names, and their trademak Sunglasses At Night. It makes sense!
 * Except Nigel in permanently bald...
 * The hair is actually a tattoo done by a really good artist.
 * Or the Nanites did it.
 * Or he discovered Rogaine somewhere along the path to adulthood.

The show takes place in the same universe as the game Jak and daxter

 * Both nanites and Dark eco share an ability to warp and mutate.Only one can control it.
 * So everyone eventually turned into elves and Ottsels?

Peter Meechum has valuable information.

 * At the end of the second episode, Six comments that eventually Meechum will talk about what Van Kleiss wanted with him. Meechum hasn't been discussed since that episode. Whatever he knows, it is vital to Kleiss's Evil Plan and it will be revealed soon before Kleiss reaches that critical point in his Plan.

Each of the Pack were designed to correspond to a mythical monster.
More of a meta-WMG than an in-story one, but still, think about it: The only one who doesn't fit the pattern is Breach.
 * Van Kleiss=vampire
 * Biowulf=werewolf
 * Skalamander=dragon
 * Circe=siren
 * Her pale complexion and malnourished appearance could suggest a zombie.
 * Or, given her schoolgirl looks, she's based off a Japanese spirit. An onryo, to be more specific.
 * Skalamander is more of a Lizard Man to me.

White Knight will turn into an EVO, as a sort of Karmic Transformation...
...And then die by what he created to destroy every last one of the nanites.

Annie will become Rex's second love interest

 * Rex said she was cute and nice. More than once.
 * Not only that, at the end of the Wingman episode, after a little aruging, Rex implied he would go out with Annie if Noah asked Claire out again.
 * Certainly would make for an interesting Love Triangle if Circe came into the picture again while Rex is seen with Annie.
 * Or what if it was BREACH who came back instead?
 * Alternatively Rex will start spending more time with Annie, Breach will come back and be locked up at Providence where Rex will occasionally visit her, and Cricket will join Providence to be closer to Rex. And THEN Circe will come back.
 * OR Breach will get to him first, get rid of Circe through a portal, and grudgingly share with Cricket, who seems nice enough. All doing this while Van Kleiss and Quarry plan their evil schemes.
 * There's also Green Fist Girl to compete with now. I think it has the Dating Catwoman elements, but less with the mortal enemies bit, more with the dating.

Hunter Cain lost his family to EVOs...

 * And one of them may be either in the Pack or a character we haven't seen yet.
 * The episode was released on YouTube and it is said that Cain had a wife, but she turned EVO.

Hunter Cain lost his family when they went EVO and he had to kill them.

 * It's why he doesn't trust Providence or Rex, when his family went EVO, they weren't there and he had to kill them.
 * He had a wife, as said above, but she turned EVO. It was never said if he killed her himself. But this could contribute to his distrust for Providence, because he said to Rex, "You push hope when there isn't any."
 * It also explains why he refuses to admit that EVOs can be cured, he's trying to convince himself that killing her was the only thing that could be done and there was no other option or chance she would be saved.

Annie is an EVO

 * Her nanites project some sort of energy field around her that distorts probability, causing her to be a walking bad luck charm. Unfortunately, she can't turn it off, and probably doesn't even realize what's going on.
 * This troper can't be the only one who thought that SHE was the bunny, and changed when angered. Then of course, I'm sure many imagined Rex giving her one it's feet for good luck.

Rex's powers change every time he blacks out

 * In Rabble its mentioned that Rex wasn't able to use any of his Shapeshifter Weapons when he was with the other EVOs the last time. And seeing that the people who made Generator Rex made another series with a chronic case of New Powers as the Plot Demands, it seems like this might happen to Generator Rex as well.

Rex's brother is the cause of his blackouts

 * Basically, its possible that something really bad happened to Rex's brother before the series began, turning him into an EVO and possibly a future Big Bad. As Rex tries to unearth his past after each successive memory loss, he finds out about his brother, tracks him down, and BAM! Right back to square one.
 * Being trapped at Ground Zero during the Nanite Event fused Rex and his brother into one body. Their shared brain can't retain two sets of memories, so whenever one of them takes control, the other one loses their memories and "goes to sleep" until the next time they switch.
 * Wouldn't that mean his brother is evil, since he would have sold out the group in "Rabble?"
 * Yes.
 * This just blew my mind.
 * All Jossed. Rex's brother has been in relativistic time-dilation since The Incident, and only 15 minutes of busy hotwiring have passed for him- he isn't responsible for any of what has happened since the initial event.

Evo mutations are "contagious"

 * When a person (or animal/plant/whatever) "pops", the newly activated nanites within their body immediately search for other active nanites, which, unfortunately, are only found in large numbers in EVOs. If an existing EVO is within range, that's set as "normal" and the body is modified to that form. If there isn't an EVO in range, the mutations made using data from the trace amounts of active environmental nanites.
 * Wait, in that case wouldn't Hunter Cain be right?
 * Check the part about "trace amounts of active environmental nanites". If this theory's right, the safest thing for everyone is to hang out with EVOs who kept their minds, and hope the relevant code gets passed on if you "pop". Er, no, wait, the safest thing is to carry a blood sample from a sane EVO, or anything carrying their active nanites in a form that newly activated nanites can access.

Phlebotinum Overload is the cause of Rex's amnesia.

 * Think about it. According to the EVO street rats, he was able to cure EVOs even back then. But we know from the episode "Frostbite" that this involves absorbing an EVO's active nanites, and if he absorbs too many, Body Horror happens. Providence treats him by removing the extra nanites, but what happened before he joined Providence?
 * See the 'Van Kleiss is Rex's Excess nanites' WMG
 * His powers would go out of control and he would turn into a biomechancal Humongous Mecha.

Hunter Cane will pull a Heel Face Turn

 * He'll go EVO, and Rex will save him. There are none so fanatical as a new convert.
 * Or, His wife, who is being detained by Providence as an Uncurable, can be cured by Rex's new Super Nanite.

When Rylander and Van Kleiss inevitably reappear, they will have been fused into a single entity
The part that is Rylander will then commit suicide by Rex.
 * So far, seems to be Jossed.
 * But what if being fused with Rylander was what changed Van Kleiss' nanites?

ZAG-RS is the one who gave Hunter Cane his weapons.

 * The episode with Cane actually takes place sometime after Gravity. Because of the damage she suffered in the previous episode, ZAG is unable to be a serious threat on her own, so she gave Hunter the blueprints to creat the EVO killing weapons (which seem similar to what ZAG was planning with the nanite suppressent in Gravity) and sent him out to do her dirty work. Eventually, ZAG would have betrayed Hunter, revealing that he was indeed infected with Nanites and would have to die.

Van Kleiss is going to cause another Nanite Event in an attempt to get his powers back

 * We know he has connections to the first one, after all, and he did say that now he'd be using his intellect, calling it his "most dangerous weapon". What could be mroe intellectual than developing a new nanite strain?

Van Kleiss' true power is...

 * He's the lead singer of Orange, the band that made the show's themesong. Once he reunites with his band, their song will bring the world to it's knees....

Circe is a Providence agent.

 * She's a really good spy, sent by White Knight to gather intel on Van Kleiss. Catching Rex's attention was just a bonus.
 * Oh boy, if that's the case, Rex is either going to have a major Heroic BSOD or do something really stupid to blow her cover if found out and tried to contact her.

Providence contracts go to the lowest bidder.

 * Every piece of technology used by Providence(guns, airships, space elevators, power armor, robots, buildings, nuclear weapons) looks like it's made out of cheap plastic. Either the economy is far worse after the nanite incident or White Knight keeps an iron fist on the purse strings.
 * Because it's Twenty Minutes Into the Future, everything looks like an iPod. Except the the animation style of Gen Rex makes it look like plastic instead of metal.
 * Supported by Caesar, who comments that the console in their main ship is made by a company that does good work, but its stuff is known to overload and explode.

Rex will use the knife Six gave him for his birthday to stab Van Kleiss.

 * Seriously, what use is he gonna use a knife with sentimental value for?
 * ...cutting Holiday's cake?
 * Trying to cut Holiday's cake. For all we know it snapped on the attempt.
 * See the "Agent Six will soon turn into an incredibly powerful EVO, forcing Rex to kill him" WMG above.
 * As a sidenote, Six is supposed to kill Rex if He becomes insane, right? Maybe Six is supposed to kill himself right after he's killed Rex?

Providence was a PMC group before the event.

 * It would explain why they didn't have any established ties and were just swooping in and snatching up EVOs. Knight was the leader, but allowed for the scientists and Dr. Fell to carry on whatever research they wanted. But as seen in "Promises, Promises", we know that there was a big regime change.

Dr. Fell will return...

 * And be working with ZAG-RS, and possibly even Hunter Kain. They'll form a competitor to Providence, and lead a campaign that will have Rex and the others scrambling worse than when Kain was on the loose. ZAG will remain their little secret, much like Rex was for Providence, and obviously plot the destruction of everyone, including her two 'collaboraters'.
 * Alternatively, Fell could be the one who designed Kain's weaponry as a means of getting back for getting the boot.

Bobo is actually a man

 * Turning EVO gave him fur and opposable toes. He just poses as a talking chimp to escape any responsibility.
 * The Librarian?
 * Jossed. Robobobo reveals that Bobo was a Chimp before and after going EVO.
 * Rex still sounds unconvinced by his alleged origin story.

Gatlock was working for Van Kleiss

 * Considering that he seemed interested in the nanites for their monetary value, and considering who's in the market for active nanintes, it seems quite possible.
 * Certainly a possibility. Though it'd be pretty funny if they turn out to be related. I mean, both basically had similar powers (mechanical arms), only Lock could make both arms change, and may not have regenerative powers like Van Kleiss used to.

Gatlocke and Van Kleiss are related by blood in some way

 * They both seem to have British accents. Besides, he could have been doing favors for him, such as getting those nanites. And since when do you see more than one British villain in the same show that isn't related with someone?

Gatlocke is Rex's brother
Suggested for the following reasons:
 * Rex is known to have a brother that he saved with his powers. Possibly some nanites transferred over in the process?
 * Both Gatlocke and Rex have the ability to generate machines out of their bodies at will, while almost all other EVO mutations are Body Horror based.
 * What better way to hide a plot critical character than disguising them as a one shot villain in a filler episode?
 * To this Troper, it seemed more like Gatlocke was a cyborg with artificial arms, especially since he couldn't repair the hand Rex tore off. That's also why I think he made the comment 'I've got EVO-envy!' as in, he would like to be an EVO, but isn't. Gatlocke is one of my favorite characters in recent media, though.
 * Jossed.

Abysus is the location of the original nanite event.
Thus explaining the nanite infused soil. Van Kleiss was at ground zero because....well, pick a WMG connecting Van Kliess to Rex's past.
 * Pretty sure Van Kleiss said so in the first episode.
 * I though the location of The Event was in South America? Where the rest of the research facility was?
 * Confirmed. The research facility was in Abysus; the lab in South America was evidently a newer sublab Rylander set up after escaping.

Breach is a human Gellert Generator
Those are actually portals into the Immaterium she's creating, and she is able to hold a whole town stable in the Warp. Of course constantly jumping in and out of the Immaterium has made her completley Barmy.

White Knight is compromised somehow
Had he finished stomping around Biowulf and the other EVO before Rex cut the power to everything in the season finale?
 * His suit power supply is presumably internalized and is definitely insulated against nanites. Rex's shutdown wouldn't hamper his performance.

Breach knows that she is both fictional and the shows Ensemble Darkhorse
She was sent to our world when she blew up and saw how unhappy she made the fans by leaving so she found a way to come back. Knowing people love her because she has little screen time, she is careful not to draw too much attention.

At some point in the series, we will meet Five
Soon afterwards, Six will have to change his name.
 * Bravo sir, for saying what no one else had the guts to say.
 * I don't get it...
 * The next episode, "Divided by Six", is supposedly about
 * They met Five, IV, Trei, Dos, and (technically) One. So...confirmed?

Six's name is really Six
As in, it's not a code name. He's French or German. (There are around 50 Families in the US with the surname 'Six'. The surnames Two, Eight, and Ten also exist, btw)
 * The 'sixth deadliest man in the world' was just a rumor made by Bobo.
 * A false one, because everyone knows he's number one.
 * Apparently Six IS the sixth deadliest man in the world. However, deadliest isn't the same as most skilled...
 * Hey, that's true enough. It takes a lot of training (often years; months if you're some sort of prodigy) to master sword techniques, but using it is only as deadly as the extent of the sword wielder's reach. Firearms can wreak much more death and destruction over a much wider area, but one can attain basic proficiency with them in weeks (for example, the US Army Basic Combat Training is nine weeks) or even days.
 * Deadliness probably also encompasses not just the ability to kill, but the willingness to do so. Six seems to have more restraint than many of his brothers-in-arms when it comes to the use of lethal force

White Knight's accident not only bleached his skin and hair...
... but also his mind, riding him of most of his emotions and making him a being of almost pure logic and rational thoughts. Which is actually a bad and a good thing, bad because it means he can't relate to the people under his command and has a tendency to alienate them, but good because it rid him of his hatred of EVOs, which enabled him to see the potential in Rex's power : added to his unique situation of being completely nanite-free, Rex's power to cure EVOs enabled Providence to receive funding and the trust of the rest of the world as an organization that could really solve the nanite problem.
 * This is actually a very credible theory. Bravo for putting it up. For any who would accuse White Knight of Fantastic Racism remember that he only ever said he didn't trust anything with nanites, he never said he hated them. And not trusting anyone with nanites is a very sensible and logical practice, when you remember they could turn at any minute.
 * Would be more plausible if he didn't keep throwing the word 'Freak' around.
 * And that this makes the least sense of any WMG i've read recently
 * I'm gonna have to call Straw Vulcan here. Logic and rationality don't work that way. There have been many instances of him showing irrational behavior, nor does being purely "logical or rational" render one incapable of understanding emotion or basic social convention. In fact, his alienation of his subordinates actually proves that he's behaving irrationally. What you've described is a lack of empathy, which is independent of rationality. Many serial killers, sociopaths with a proven lack of empathy, manage to avoid detection for so long because they were rational enough to analyze and understand basic social protocol and human emotions, and react appropriately to them even if they didn't truly empathize. Many of them were even described by neighbors are friendly and charming. Contrast White Knight's behavior where he has -- time and again -- pigheadedly acted in a way that only caused Rex to rebel further, even though the rational option would be to try and reason with Rex instead of bludgeoning him with authority since even a cursory analysis of all of Rex's previous behavior should clearly indicate that he responds better when he's allowed some leeway than when he's held on a tight leash.
 * Alright, I will accept the charges of Straw Vulcan and admit I spoke of things I didn't really know about. However, I would like to maintain the core of my WMG : that accident did something to the Knight's mind. Took out part of his emotional side, made him extremely 'cold', made him near incapable of empathy. If you've played the video game The Longest Journey, I base the whole thing on the character of.

Breach Will Heel Face Turn
A guy can dream.

Honestly, nobody would bat an eye if Breach got some ultra-sympathetic backstory, and with such sympathy, comes a much greater chance for redemption. Taking into account her Ensemble Darkhorse status and the fact that this is a kid's show, its a lot less likely that redemption would happen in the traditional fashion

ZAG-RS and Knight will become a couple
Are you disturbed yet?

The Bunny Rabbit EVO from Project WINGMAN really is Rex's Arch Nemesis.
That bunny is one of Rex's old enemies, with a rivalry that goes back years. Rex doesn't always remember thanks to his black outs. It's been dogging him since almost directly after the Nanite Event. That's why it stalked him everywhere and knew just how to fight him. Every few months, they cross paths and fight till one ends up in a situation where No One Could Survive That if Rex remembers or not. In fact, the first entry in his old pocket video journal was something along the lines of "Look out for the bunny."
 * Like Peter and the Giant Chicken? Maybe it started out as small rabbit he tried to hunt in the slums of Hong Kong that went EVO?
 * Whoa, this actually ended up semi-confirmed. It's a family of giant evil rabbits instead of a single individual, but yeah.

Skalamander's whole fammly whent evo and he's the "lucky" one.
They are all mindless horrers expect for him. Way, it would be a cool twist.

Dead Space takes place in the far future of Generator Rex.
It wasn't DNA on the Marker, but nanites. Providence discovered, and sealed up the Marker, then destroyed all records of its existence after discovering they didn't have the technology to destroy it.

Nanites act as a a Jackass Genie in a way.
They for the most part give the affected person a twisted version of what they want when they were infected. Here are theories as to what I think their wish is
 * Rex = Wanted to escape guilt from somthing
 * Van Kleiss/ No face = Become a leader
 * Breach = Wanted to travel
 * Circe = To be a singer and attract boys
 * Noah = Wanted to be be free to have fun when he wanted
 * Random beasts = to not be hunted by predators
 * Purple guy in a suit = He was a glutton

Tuck, Cricket and Sqwydd were partially inspired by Team 8.
My only reasons for this is that both Cricket and Hinata are Shrinking Violets with feelings for the main characters and Man Of Action shows have had many Naruto references before.

White Knight is a Time Lord
It's not a WMG page without at least one of these. His TARDIS has been damaged by nanites, and that's why we don't see it. The entire series is a Xanatos Gambit to get him the tools necessary to fix it. Alternately, Breach is Haruhi Suzumiya with a bad case of Ax Crazy.

Six is a Cyborg
First and foremost, his name is a number. This is normally indicative of an android or mechanical being. Also, he is shown as being by far the most powerful human on screen, going far beyond the established limits of other characters. And to add fuel to the proverbial fire, Serge said his name was that of a machine. And Rex's/Six's immediate redirection of the conversation indicates some foreshadowing just went down.
 * Six's handle is because he is the sixth most deadly person in the world, which is also due to his insane physical abilities. Also, Serge was referring to Six's stoic nature and the fact that he followed orders without thinking for himself, as a machine would.
 * But he does think for himself before following orders
 * Not as far as Serge knew. He only knew Six for a few minutes, which were spent by Six considering how to best destroy Serge's home basically.
 * Jossed, at least as far as Rex knew, who commented in "Waste Land" when Six tells him that this Sea-Urchin would have killed a normal Person, 'You know WAY too much about stuff that can kill you, Six.'
 * Jossed. Six reveals in "Divide By Six" that

Circe's figure is part of her powers.
She used to be fat, ugly, or she had some other physical problem. Then she became an EVO, and not only did she keep her mind, but it actually made her more attractive, instead of less. This is why she says "I Don't Want To Use My Powers" instead of "Please Cure Me, Rex", because being cured means going back to how she looked before.

Breach is Monoko, several years older and after manifesting physically from Madotsuki's mind
Breach looks a hell lot like Monoko, only minus that extra hand on the head and the stomach swirl. Not to mention controlling portals sounds like a very dreamlike power.

No Face escaped the Bug Jar at the end of the "Alliance"
We never see for certain that he was in there when the force field went back up. It would be a shame to waste a cool villain by leaving him trapped.
 * Related Theory: He and Circe will join the Green Fist, allowing more Dating Catwoman moments for Circe and Rex, and giving Rex and No Face a chance to work together.

The Nanite Event happened in 2005
In the comic there were occasional visions of a mechanical cataclysm in the Future, the future being 2005, perhaps that was related to the Nanite Event. Of course it would mean the series takes place in 2010

Providence will undergo a Face Heel Turn
It's an organization that is funded by various governments, patrols an entire post-apocalyptic world, uses state of the art monitoring equipment to both detect EVOs and watch Rex like a hawk, and is currently run by a guy named White Knight. EVOs, while mostly raging monsters, have gotten more and more screen time lately depicting the more intelligent ones as "different, not evil" and constantly remind us "Providence isn't the only option." Clearly, they're being set up as the true villains of the show.
 * Rex, Six, Bobo and possibly Holiday will go AWOL after Providence crosses the line in their crusade to rid the world of the "EVO menace". They will then not only have to fight rouge EVOs, but a highly militant Providence with a nice bounty on their heads. Along the way, they'll meet and team up with various good EVOs for a later Gondor Calls for Aid moment in the finale. White Knight may or may not struggle with the direction Providence is taking, and if he does have a Heel Realization, he will be promptly replaced with someone worse with the last name "King."
 * Certainly would be intesting. Of course, don't forget that Rex (and Bobo, to some extent) are quite chummy with most of Providence, so it could wind up they have to go on the run, but eventually regain a foothold with the soldier they've befriended over time.
 * So it would become a case of the Big Bad Government vs Rebels who have the sympathy of the Big Bad Government foot soldiers? Real Life Much?
 * Confirmed. After the time skip, Black Knight takes over Providence and directly opposes Rex. Or rather, Rex opposes her.

Bobo's was Curious George
His origin is 100% correct, but the color was a man in Yellow not Purple.
 * Maybe it's a shout-out, but the color was changed for less legal hassle in the future.

Hunter Cain's wife was named Caroline
You didn't really think he named his BFG after the song, did you?

There will be a Cross-over between Generator Rex and Ben 10 eventually
If only because it would be awesome to see Who Would Win with Rex vs Ben.
 * If you mean original Ben 10, then that'd be a fun What-if scenario. Otherwise... no, I'd rather see Rex go anywhere near that traninwreck that claims to be Ben now.
 * Definitely original Ben, unless it's a Take That Me BLAM Episode with it's tongue firmly planted on the cheek.
 * I don't see hot it could be a Take That Me, since Man Of Action had nothing to do with the later reincarnations.
 * Confirmed. It will be part of the GR continuity. It's going to be interesting to see how Man Of Action writes aged-up Ben.

Cesar will turn bad.
Either because of his seemingly crazed nature, or Face Heel Reveal, Cesar will turn out to be a serious threat. For one, Van Kleiss did seem a bit pertubed when he realized Cesar was alive and well, and it did seem odd that Cesar didn't just say "Hey, could you guys drop me close to the ground?" when he helped out with the starfish evo. Of course, he really could just be touched in the head and will eventually snap out of it when the time comes.
 * Six revealed a few seconds later that the Providence soldiers would NOT have dropped him off had he asked. But if he was able to discern that so quickly, then you're right, something about Cesar makes him Dangerously Genre Savvy.
 * Seems like we do have good reason to have suspicions. If Written in Sand is any indication, he certainly seems to be full of secrets. Though I wonder if he might be possible suffering from a sort of split personality.
 * Confirmed-ish. While Caesar does work for Providence (Which has undergone a Face Heel Turn), it's hard to call him 'bad'. The mind control collars are a genuinely good idea.

Rex will lose his powers for good in the finale
Somehow, all the nanites will either be destroyed, or permanantly reprogramed into a harmless state, but at the cost of Rex's ability to build any more machines. Granted, by this point Rex will be perfectly fine being a normal human, free of the burden of his powers. Then it'll be poked for laughs when he realizes he can't breeze his way through school or sports as he finally settles into an ordinary life.
 * With Noah, who is top 4 in his class WHILE hanging out with Rex tutoring him, he'll adjust in no time!
 * This is in a lot of fanfics, I'm just saying.

If they ever make a Generator Rex videogame
According to certain articles, Activision will be handling a video game adaption, though no word on whether any of the crew from Prototype will be involved (though it'd be amazing if they were, given how Rex is similar to Alex Mercer). In any case, the game should be an open world sandbox, with either an unnamed city or state as the hubworld (where the main plot is focused). Rex would be assigned missions and then have the option to choose which ones he takes first, their success earning experience skills and upgrades to Rex's builds. A psyche/stamina meter would affect how long Rex can use his machines, and when/if he can (to add tension in harder/scarier parts), meaning that Rex will have to be psyched up to use his powers without fail. Hopefully by the time the game is released, Rex will have a sufficient amount of builds (though likely some will be added in the game, and possibly become Canon Immigrants) so that there is plenty of variety in which powers players will be able to use (barring the likely DLC that would come along as well).

The biggest question is, will the game be a hard T, or suffer from the dreaded restraint of an E rating? We know the series is far from kid friendly (at least little kids), but it'd be a shame if Rex is just smashing robots half the time and not dealing with any major threats. Conversly, it would be nice to see a hardcore game that doesn't rely on just mindless blood and gore to be good.


 * Problem is the game would just be Prototype !FOR KIDS or Prototype Lite, though if it improved on that game's many drawbacks (ugly graphics and annoying mission design most notably), it could dance around The Problem With Lisenced Games. Personally I'd think Cel Shaded graphics would be really nice.
 * Huh? The graphics in Prototype weren't that bad (granted not nearly as polished as inFAMOUS, but chalk that up to it being made concurrent for two systems). But it still could be fairly violent (long as Rex's enemies are monsters with non-red goo blood). But you never know, hopefully they'll be bold with this and actually break the curse on licensed games based on cartoon (and I mean, if Batman could, then why shouldn't Rex?)

A real Eldritch Abomination will appear sooner or later.

 * It's possible. I mean, if the Chupacabra is real in this world, who's to say that a Cthullu expy isn't far off?

Cricket was a former prostitute.
She is said to have a crush on rex because he saved her from a bad situation, and i can't think of anything worse.
 * Certainly a possibility. Though the show probably won't be able to say anything like that. Though they could at least imply it, if Cricket ever gets a second appearance.

Rex will eventually finish the programming on all the Nanites in the series finale
ZAG-RS already showed destroying all Nanites isn't an option. Rex's Nanites are fully programmed and that's why he can control them. In addition, his can control others. So he'll finish all the programing of the nanites and use it to turn the world from a Crapsack World to a wicked awesome one where everyone on Earth has awesome superpowers instead of the Body Horror mutations they have now. Yeah, there'd be some people who use them for bad, but that's what it's like now, only difference is they're less of a threat if everyone has powers and there'd be a lot more superheroes.
 * At the very least it would mean everyone would be in good health with diseases like HIV and cancers kept down by the reprogrammed nanites.

Concerning Ceser being possibly evil
It's possible that he may be a Well-Intentioned Extremist who wants to save his brother, but is willing to let everyone else suffer if it achieves his goals.
 * Personally, I think Caesar and his parents were the scientists who wanted to use Rex as a weapon. It would make a nice twist, no?
 * So maybe ZAG-RS really is their mother with her mind uploaded into the machine? That'd be pretty crazy.
 * I'm figuring it'll go down in one of two ways: Cesar is playing The Chessmaster, and is doing a bang up job pretending to be Cloudcuckoolander. Or He really is whacked out of his gourd and is suffering from split mind, where one half is the friendly but clueless brother, while the other is a cold hearted bastard who makes Van Kleiss look like Jesus.
 * Who's to say he isnt a Cloudcuckoolander and The Chessmaster, the two don't have to be mutually exclusive. That's why Bunny Ears Lawyer exists.
 * Personally, I believe he's a genuinely sick (as in having a pyschological disorder) individual.
 * Seems to me he is just a Badass Bookworm with ADD.

Doctor Holiday is the daughter or granddaughter of Elspeth "Doc" Holliday
They're both scientists working for an outfit that deals with unique threats (EVOs and the supernatural respectively) and they both have a similar sense of humor which could be a possible case of It Runs in The Family. Both of them also work alongside an enigmatic Man In Black.

Van Kleiss had some sort of relationship with Rex and Cesar's mother Violetta and Cesar knew/figured it out some way.
Van Kleiss worked along with Rex's family and his tone of voice in the previous episode suggests he had a fondness for his mom. Its been suspected that Van Kleiss is Rex's father by some fans and that may not be entirely implausible. Rex might be the product of a brief affair between the Van Kleiss and Violetta that her husband never knew about. Ceasr may have discovered this sometime before the Nanite event but said nothing to is father or Rex out of his love for hi mother. From what we can gather in that episode as well, Cesar was very close to his mother. Or Rex isn't Van Kleiss's son and he and Violetta didn't have an affair but Van Kleiss loved her and perhaps he blames Caesar and maybe even Rex for her death.

Caesar was the one who arranged for Hunter Cain's release.
Hunter Cain said that someone within Providence paid for his release. White Knight is too obvious as the resident EVO-hater and has already showed distaste for Cain's methods. Doctor Holiday, Six, and Bobo are extremely unlikely, Captain Callan is too dedicated to Providence and is trusted by White Knight (Since the moment Rex fails, Knight always sends Callan in to finish the job.) Kenwyn Jones might have been likely if not for her Character Development, and so...the only one left is Caesar. Mostly the theory is that Caesar had some kind of plan for Cain, but Cain went off to do his own thing or was contacted by the Mayor before Caesar had a chance to contact him.)
 * There's also the unidentified Providence traitor that Van Kleiss was in contact with at the beginning of "Payback." We never did learn his identity, anyway...

Violetta Salazar is...
Doctor Holiday's sister. Simply because Doctor Holiday being Rex and Cesar's mom is too obvious, Plus, what better way to bring back the character?
 * Jossed as of A Family Holiday--Holiday's sister's name is revealed as Beverly, and she seems to be around Rex's age.

The nanites are Level 4 Technology or higher
. The Event provides a pretty good example as to why humans, at the moment, are only capable of handling Level 2 Tech at the most.

Circe will become a Big Bad
Rex will probably kill Van Kleiss for real, leaving Circe traumatised and mentally fractured. Using her powers to their full extent, she'll seize control of the Pack and all other Evo's in Abysus and use them to try crush Rex and Providence as revenge.
 * Not possible or likely considering the current status quo.

Hunter Kain will go after
.

Because the man's entire schtick is that EVOs cannot be permanently cured, which  clearly shows to be the case. He may not believe she's cured or may not even care. Expect an all-out war between him and Rex's crew, especially.

Breach's Epic Fail is actually...
... a Flawless Victory for Van Kleiss and the Pack. Quarry's abduction is another part of a master plan that Van Klyce is brewing up, a plan that started when he stole that reactor back in the first episodes. The Pack didn't really want that weapon, they just needed to 'get' Quarry for that master plan. Breach's last smirk to the viewer wasn't seen by Rex & Co, and wasn't an animation mistake either. She was simply satisfied with a mission that went perfectly as planned, the personalities of each of the pawns exploited to their full potential, the Pack off with what they wanted, and Providence not having a clue of what's really going on.
 * Jossed by the episode 'Remote Control'.

The EVO statues in Van Kleiss's garden are...
Two of the three scientists that wanted to weaponize Rex, because they were seen in his dream in Frostbite and they look exactly the same as the EVOs in the garden when the sequence changes... or they could be Violeta and Rafael Salazar, just 'cause.

The Nanites are just doing what they're programmed to do
The nanites were supposed to repair damage and cure diseases, but the code that restricts them to the organism's baseline is faulty. Instead of just restoring their host to a healthy state, they go further and try to "improve" the organism. The EVO's practically always turn into oversized predators because, from the nanites' perspective, bigger, stronger and more dangerous is a logical improvement for the host. The EVO's are superstrong, superfast and often take on forms based on their environment, such as the desert priest who transformed into a cactus-like creature and the fisherman who became an aquatic EVO, and they often gain superhuman powers, like Breach's portals or Circe's screams. This is especially clear with animal EVO's like the beetles in "The Swarm": being bigger, stronger and faster at reproducing, they can outcompete normal bugs and take their ecological place. Each person and creature's nanites, once they "pop", try to improve the host as much as they possibly can. It's just that the human mind often can't withstand the process, so most EVO's turn out as mindless beasts (which the nanites, only being programmed to repair the body, don't worry about).
 * Also, Rex's Nanites had their programing completed, and ended up with superpowers anyway. So it's possible that improving the base organism was part of it from the beginning, but the nanites take that too far too.

The 'RS' in ZAG-RS stands for...
Rex Salazar. And she was used to remove Rex's excess nanites prior to the event. Or had some sort of affiliation with Rex.

Cesar is the one who...
Caused Rex's blackouts. He was able to gain control over Rex's nanites and somehow wipe his memory like he probably did ZAG-RS's. Rex witnessed Cesar cause The Event, and at the last minute his older brother wiped his memory in fear of being found out. Cesar then proceeded to get on his spaceship. He also wiped ZAG-RS's memory because she held harmful data... or something.

There were some fully programmed nanites released in the explosion
This is why some Evos merely gain superpowers and don't mutate into a monster. Ones like Bobo and Circe are infected by a mix of fully programmed Nanites like Rex and unprogrammed Nanites like everyone else, the programmed ones preventing them from being completely mutated. Van Kless is probably infected simularly, but when he was revived, his programmed ones were corrupted, letting Rex cure him.

Providence but Rex specifically is assembling a Chekhov's Army
- I thought it about more in a recent episode "Nightfall" with him and his "family" down in Mexico, He interacts with a whole slew of characters both evo and not each with special talents and powers that would be amazing in a fight against Van Kliess. I'd be really disappointed if the series finale didn't have something like that.

Rex selling Quarry to The Pack was the whole goal of the Hard Target plan.
After the disaster that was the negoitiations with No Face, Van Kleiss decided his next partner should be firmly under his thumb before the talks could begin. So after learning of Quarry's past connection to Rex, he had Breach give him the oppurtonity to wreck some havoc "against the deal", and when Providence cracked down, Abbysus would be a saviour by either saving him, or sparing him when Rex left him for the wolves to punish for his rebellion, discouraging future bad conduct. Learning where the treacherous Circe was is a bonus whose use will be determined at a later date.

Rex's amnesia will return in the Season Finale.

 * And Van Kleiss will find him before Providence does.

Night Shadow is really a double agent

 * Turns out Van Kleiss either revived him, or found him sometime before Providence came to search Rylander's old lab. His whole "revenge" scheme was merely a means of quickly sympathizing with Rex and gaining his trust.

Agent Six left because without Rex he had no reason to stay

 * In Six Minus Six, he lost all of his memories but was persuaded to stay because of Rex and the fact that Rex trusted him. Rex vanished for six months; everyone probably thought he was dead. Sp Six left. There'll be one hell of a "where were you" moment that leads to a Crowning Moment of Heartwarming.
 * Likewise, Holiday: without Rex, there was no cure. She couldn't just let them start killing again, and so went to do research elsewhere.
 * Even White might not have gone bad--something else might be going on. We don't know if Black Knight is telling the truth. Clearly things have changed...and not for the better.

Caesar Salazar is a high-functioning sociopath.
Not necessarily good or evil, but he definitely is lacking something in the empathy department. All of his emotional reactions, if he has any at all, seem very stunted and almost forced. It wouldn't be too far of a stretch to assume he just doesn't feel emotions as deeply as everyone else. What this means for his role in the series, who knows?

White Knight became an EVO
During Lions and Lambs, he was fighting Van Kleiss, and in said battle Van Kleiss had jammed his claw glove into White's power suit for a good few seconds, where even a nanoscopic tear could lead to infection. Black Knight said White was gone because he tried to stage a hostile takeover, but we have no reason to actually believe her, and saying that doesn't sound as bad as saying 'we lost the one pure human on Earth'.

Ceasar is not evil....
He's a Well-Intentioned Extremist trying to make up for accidentally causing the Event five years ago. Coupled with his obviously lacking empathy skills, is it so unreasonable to assume that while he does love Rex and want to save the world, he's slipping into "I Did What I Had to Do" territory?
 * And this will be the focus of Back in Black
 * Ahem. Beard of Evil. QED.
 * Confirmed-ish. The mind control collars serve a vital function (Especially since Rex was missing) and take the 'Kill' out of Contain, Cure, Kill, but some might see taking away free will (However much free will EVOs have, anyway) as being extremest.

Caesar's machine didn't malfunction
It was supposed to wipe Rex's memory and turning him into that giant robot thing (Caesar had a way to control him when he was like that). Caesar wanted to have complete control of Rex--what better way than wipe his memory and have him turn into something unbeatable (and as we saw, there was no way Six would be willing to kill Rex).
 * It's also why Six almost died where Rex just risked a memory reset. Caesar decided Six being back to his old mercenary self but only loyal to Rex was a liability. Or he was jealous that Rex clearly trusts Six more than him.

Van Kleiss wanted to go back in time and prevent the Nanite Event.
Hence his telling White Knight "If you knew what I wanted to do, you'd be helping me." Of course, without the Nanite Event, Van Kleiss has a monopoly on the creation (and control) of EVOs, allowing him to create an unstoppable army.

Black Knight is ZAG-RS in a human or humanoid body

 * She's either a robot, a nanite construct, or a human whose nanites have been hijacked by ZAG-RS. Caesar may have had something to do with her construction.

Caesar is, and always has been, jealous of Rex's powers.

 * 1) The accident that nearly killed Rex was Caesar's fault.
 * Not intentionally, of course. But in Tom Sawyer fashion, he suckered Rex into doing a chore or an errand that he didn't want to do. That chore, by chance, puts Rex in the right place and the right time to suffer the accident and get a nanite transfusion. If Caesar hadn't convinced Rex to do it, he would have been the one getting the operation.
 * 1) Caesar wanted Rex's powers.
 * When the operation is successful, Rex becomes the darling of the scientific community overnight. Try to see the situation from Caesar's point of view. You've been a child prodigy all your life, the son of two great scientists, working your ass off and possibly sacrificing huge chunks of your childhood for recognition in the scientific community. Suddenly, your ten year old brother - who has probably never worked for anything or accomplished anything on his own - is given the breakthrough of the century on a silver platter, and you're now living in his shadow.
 * To add insult to injury, your little brother develops superpowers as a side effect. While all this is happening, while he's getting all the attention and love and recognition, all you can think about is how that could have -- should have -- been you. After all, remember what Rylander said to Rex? "The look on your brother's face..."
 * 1) Caesar caused the nanite event because he was either trying to obtain Rex's powers, or control Rex.
 * We don't have a lot of information about what, exactly, Caesar did to cause the nanite event, or how it even happened. Still, judging by the way Caesar was dodging questions, it's obvious he was doing something he wasn't supposed to do.
 * It's been suggested that Caesar was the one who caused Rex's initial blackouts - perhaps Caesar was performing an illegal/unethical experiment on Rex, or trying to "steal" the nanites from Rex in a Van Kleiss manner to take the powers for himself.
 * It's also been suggested above that ZAG-RS has something to do with Rex, and the RS in her name stands for "Rex Salazar". It would certainly fit with the idea that he wanted some kind of control or influence over Rex.
 * The Omega Nanite might have been developed as a means of developing powers similar to Rex. Maybe that's why Caesar and Van Kleiss both wanted it, and why it was developed in the first place.

Black Knight is Breach, or a blood relation

 * Her face and hair are very similar-same pale skin, dark hair covering one eye, same colored and shaped lips. They might have the same hairstyle if Black Knight didn't tuck it behind her ears. It's either this, or an egregious use of Only Six Faces. Breach had a time machine buckled onto her, perhaps she landed in a different time than Rex, like, say, ten years in the past. After losing her extra arms...somehow (perhaps she's just hiding them; she is wearing a cloak/cape after all)...she managed to become a part of the Providence council. And she's been waiting for Rex to return from his time traveling incident ever since. This might explain by Black Knight was so affable to Rex, because she last remembered him as a close friend. She only chose this moment to take over Providence because at any earlier point, Rex would only consider Breach an enemy.
 * Pretty well Jossed in "Back In Black": Black Night was already part of Providence, and stepped in when White Knight stood against the higher-ups and went rogue.
 * Breach is a time traveler - maybe she goes back in time, gets cured, & then joins Providence. Alternatively, Black Knight becomes Breach & gets thrown back in time.

If or when Six gets a recall

 * Something will happen that triggers Rex's Super-Powered Evil Side. Maybe Six, Holiday, or someone else will appear to die, causing Rex to turn back into the giant mech from Promises, Promises. It'll all be sorted out in the end, and Rex will return to normal, but the point is that right after Six regains his memories, Rex will lose his.

Van Kleiss and Rex were very close before the Event.

 * Rex comes from a family of prominent scientists, and with a big project like the Nanites in the works, his parents and brother were all in very high demand. Who looks after their ten-year-old son, then? Well, saddle one of the flunkies with him. Caesar picked out a quiet, unthreatening, third-rate lab hack for the job, Van Kleiss. As he and Rex spent time together, they grew very close and Rex looked up to him. Then the event happened, and the nanites drove Van Kleiss insane. He can remember the attachment to Rex but it has become twisted and warped and lost in his struggle for domination.

The Nanites are sentient. Van Kleiss and Rex are both their puppets.
Though neither is aware of it.

Black Knight took over Providence, White Knight tried to stop her but failed, forcing him to go underground.
With the recent episode, its becoming clearer and clearer on what happened. White Knight didn't go rogue, it was Black Knight who did. Possibly on orders of the higher ups. Black Knight was able to convince Cesar to join her side, given they share the same mentality. Approximately two months into Rex's disappearance, Black Knight's coup d'tat started and she was able to force White Knight, Holiday, and Rex underground thanks to Cesar's inventions which control the EVOs.

Breach isn't an EVO.

 * She's another experiment from around the same time as the nanite project.

Caesar is a fan of Brandon Moses because he knew his true intentions from the start.

 * Which is how he came up with the idea of controlling EVOs in 'Back in Black'. Maybe Moses is in cahoots in running New Providence with BK and Caesar?

Cesar is an EVO.

 * Like with Breach, the nanites' mutations made him go a little funny. Black Knight found out and is currently controlling him. Because honestly, whether or not Van Kleiss was right about Cesar causing the Nanite Event, and whatever his motivations are, he's shown himself (as in "Mixed Signals" and "Night Falls") to be extremely protective of his brother. To endanger Rex's life by turning the EVO-brainwashing machine to full power, with only a token objection, seems a bit out of character.
 * He had six months of wondering if his brother was gone forever, and then suddenly his brother is back. That'll do funny things to you even if you're normal, which Cesar isn't.
 * Yeah. Besides, Caesar seems like more of an 'The ends justify the means' kind of person. Although we'll probably find out there is some kind of horrible side-effect of the mind control later on, the mind control IS a pretty good solution, all things considered. The only real problem is that the collars can be deactivated at any time by Black, which means that she could potentially re-release the controlled EVOs into society, then threaten to turn the collars off if she doesn't get her way. Basically, she's successfully managed to weaponize EVOs, just like Van Kleiss...

Rex's memorys are like ROM in a computer, due to the vast number of nanites.
The only difrence is his human side won't entirly let go of the memory so it instead will be stored in his nanites. The use of his nanites, mostly when his creations are broken apart, is what cause his memory loss, as nanites containing his memory are used up. The rest of the memory will eventualy be lost as well because the nanites take the place of blood in his body and in turn will be replaced by other nanites, as old blodd cells are replaced by new ones, made from the Omega, and will be in lack of his memories. A possible cure to his eventual, and inevitable memory loss, is to program the Omega nanite, to store his memorys, so that when the new nanites are created, they will have his memory.

Rex is the cause of all of the nanites in the world, still.
The nanites, like blood cells, die eventually, and only one person still makes them. Rex with his Omega nanite. The Nanites escape through his pores, and when he transforms and, being so small, are swept up into the atmosphere, like small dirt particles, that future rain droplets form around. Pouring back to earth in the trillions, Rex contiues to feed the EVO problem. One potential cure to the overall nanite problem is, well simple and cleanly put Rex's death.
 * One problem: Rex didn't have the Omega nanite until halfway through the first season, and things were already going downhill before that. Plus, he's been shown to develop nanite overload, which wouldn't happen if he was constantly leaking them.
 * I would say he leaks them too slowly for them so not build up, but you shut me down with that Omega nanite info. I didn't know that, thank you.
 * Actually...you were right-ish. The Omega nanite does apparently create nanites according to Heroes United.
 * Actually...you haven't been paying attention. Read what I said above: Things had been merrily going to hell before "Dark Passage" (season one, episode nine), which is when Rex received the Omega nanite -- and the Omega nanite's abilities were spelled out in "Written In Sand" (season two, episode 12; fully ten episodes before "Heroes United"). Rex couldn't access the nanite production ability before S 1 E 12, so unless the OM 1 makes nanites on its own, even while it's in storage in the jungle, Rex is not the source of all the nanites, still.

Van Kleis has the ability to drain nanites just like Alpha.
In one episode the crew was fighting an EVO in their H.Q., Providence, when out of the blue, a statue of an EVO turns to life. It's revealed that the EVO had a run in with Van Kleis who I'm assuming tried to drain him and wasn't as sucesful as Alpha. Which brings me to the connection. In the Mash-up episode Alpha would drain evos to dust, the stage they would reach before dust was (you guessed it) rock like.
 * ................ You weren't around for the first half of the series, were you?

Alpha is the same Alpha from Men in Black.
They have the same name. They have the same accent, and pretty similar voices. They are both hell bent on destroying Earth. They were both sent away after betraying their creators and friends. It make sooooo much sense.

Like Rex's nanites, Van Kleiss' nanites weren't from the same source as everyone else's
However, instead of the programmed nanites, his nanites were made to replace Alpha after Caesar sent him away. That's why he's unstable and can drain people's nanites. Meh, I know it's underdeveloped, buut... Work with me?
 * The Omega One nanite was created to take Alpha's place, and Rex has that. The rest of the theory works for me, though. Van Kleiss was working in the lab; maybe he programmed his own batch?
 * Or just knows about them to modify them? The draining peoples nanites is likely an application of his knowledge, the glove was made by him and is not part of his natural EVO powers (controlling living things with nanites in them)
 * He could only create and control EVOs after he uncured himself at the end of season one. Prior to that, he only had control of the ambient nanites in Abyssus.

Face Heel Turn Providence isn't very unified
Remember in Crash and Burn when the Providence soldiers going after the bikers tried to warn Rex that he shouldn't stick around (and possbily be captured)? Is is so much of a strech to say that some of them remember Rex's work and want things back to they were under White knoe that they know he's back?
 * Maybe there'll even be a schism soon...
 * The current Providence soldiers don't seem to be the same ones that worked for Providence while Rex was around. They're extremely competent now, for one.
 * That may be Black Knight's influence. Some of the foot soldiers seemed to know Rex, which means they'd been around before the time skip.
 * Confirmed. "Black and White" shows that Captain Calan and a number of his men are White Knight's inside men. Calan is even loyal enough to smilingly take a punch to the face from White Knight to make it seem like Calan tried to fight them off instead of letting them in.

The episode "Double Vision" will be hella creepy.
Description from The Other Wiki: "Van Kleiss teams up with Black Knight in her relentless efforts to capture and control Rex." It's like an Affably Evil sundae with a Memetic Molester cherry on top.
 * And now the description is something about Rex losing his goggles. Say wha?
 * The quoted description was the work of a Wiki Vandal. Losing his goggles is the correct description.
 * Dang.
 * The EVO everyone was fighting was pretty disturbing, though.
 * This episode likely took place before the Ben 10 crossover, as it would explain how Rex's goggles function like a tool rather than just be sporty protective eyewear.

Six Will Still Go Papa Wolf Over Rex at Some Point, Despite the Amnesia...
And it will be even more awesome and terrifying than any previous time due to it being amnesia!Six. Rex will probably be somewhere before "yep, he totally still cares" and freaked out.
 * Or, alternatively, to save Holiday.

Black Knight will be horribly injured in a one-on-one fight with Six, losing both arms and both legs.
She will then loudly insist "'Tis but a scratch" and threaten to bite his legs off.

Black Knight is a descendant of .
It's why she was so interested in finding.
 * Now that would be interesting, wouldn't it? But if that were true, wouldn't Black Knight have warned
 * Which she would have known about ... how, exactly?
 * She was a member of Providence's board of directors, and likely one of White Knight's superiors when the incident with Breach took place.

Providence is going to get a ton for bad press very soon...
Black Knight  Holiday's guide already said that the Cairo artifact guild (or whatever the association was) didn't trust her and was wary about Providence being around the monuments. That little bit of destruction was probably caught on someone's camera phone or something and BK will soon be known around the world for destroying a national treasure trove. I don't think many governments are going to be giving Providence the OK for much longer...
 * Of course, she might use those mind-controlled EVOs of hers as leverage, but who knows?

Rex's Parents were not good people
And neither was anyone else involved with the Nanite Project. Recall everyone we've seen on the show so far connected to the Project was, at best, off. Even Rylander had ulterior motives, and obviously was in cahoots with Cesar concerning that Omega nanite business. Cesar is obviously amoral, and he thinks of his mother as "comforting", but from a normal viewpoint she was likely as bad as he is, if not worse.
 * Which, of course, means he created an AI based off the woman he thought most highly of to perform a rather mundane task that spiraled greatly out of control, threatening everyone.
 * Related Theory one/both of their parents were abusive in some way...and Cesar failed to relize this. It's common for abused children to believe it's their own fualt for the abuse, so it's extremly possible that Cesar and Rex never told anyone. Since Cesar modled ZAG-RS after their mothers voice she was probably the least (if at all) abusive to them, which is why he labled the voice "comforting". Cesar's less-than-sane behaviour is the result of the abuse. On that note...

Black Knight is Rex and Cesar's Mother, Violetta.
Whether a normal biological mother or a genetic donor to the projects from which they resulted (in partnership with their "father" Dr. Rafael Salazar), she's mother to a pair of Designer Babies, one a super genius, the other a walking nanite interface device. ...she does have purple hair...

Black Knight is a long-term thinker regarding Rex.
She and Rex worked cheek-by-jowl in "Riddle of the Sphinx", but she never even referenced bringing him back to Providence. The reasons: A) She had bigger things to worry about at the moment; B) it was her and her bodyguards vs. Rex, Bobo, Holiday and Six; and C) she's luring Rex into a false sense of security re: her intentions for him. Once he lets his guard down, she'll spring. She seems like a grand planner, and Rex would doubtless play a part in whatever she came up with.

Something happened to Cesar during the event
What if Cesar use to be a perfectly sane, good older brother? My guess (if this is the case) he, along with Rex, tried to stop the event from happening but due to derect contact with his nanites he went insane (or at the very least loony). Also, currect me if I'm wrong, he was lying down in his flashback in "Mixed Signals" which (the flashback) is set after his lab went into light speed. He could've bummped his head, really hard.

The reason Rex was a jerkass back when he was leader of his old gang was because....
....he was "raised" by Spiken. (A character from the comics who hasn't made an in-show appearence yet. In the M.Rex comics Spiken is shown to be a good thief, a good actor, and a coward)He convinced Rex to do what he wanted by telling him (Rex) that he (Spiken) would help him recover his memories/find out about his past. When Rex realized Spiken was just using him, Spiken either left him(Rex)for dead, or something bad happened to Spiken(like Rex killing him in a fit of rage). By the time Rex met everyone in the gang he still remembered everything about Spiken making it so he'd "only look out for number one", which led him to working for Quarry. A guy with a lot of power who could have very easily killed Rex back then.(it was implied by Tuck Rex didn't have nearly as many builds, if any at all, back then during Rabble) Rex evevntually had enough of almost getting killed and sold the only friends he had (and to blind by selfishness to see) for "freedom" from Quarry. Quarry then attempts to kill Rex, who for the first time, used the BFS relusting in why Quarry is missing part of his face. Rex then makes a break for it leaving Hong Kong but accidentaly leaving his journal behind. After Rex leaves theres no one left to stop Quarry from makeing the gang work for him.
 * And if Rex gets these memories back he's going to develope trust issues.

When/If Rex gets at least some of his memories back it'll be in a Rule of Rose esque way
,and Breach will help with that. He'll even ask her. She'll send Rex and the others (including his old gang) into a "Doll House Just For Rex". The Keep will be the shows version of the airship, and Rex will act the way he acted in the memories he recieves back. He'll also draw something similar to Ro R's storybooks.

Black Knight is going to go EVO.
Because the whole point of having White Knight in charge was that he never will.
 * Overlapping with the "Black Knight is Breach" theory above, BK's transformation will cut her age in half, shatter her mind, and give her an extra set of arms and the ability to open portals with her mind. The only difficulty is getting her sent back in time without Van Kleiss' device...
 * This troper is starting to think she's already an EVO, and just keeping it under wraps for now. Circe (and possibly Feakins) prove it's possible to change and still pass for normal. The second part of this guess is that the Consortium is aware of it, and that's why she got the job. No idea what her abilities would be, though.

The meta-nanites can give powers linked to their part of the Dominion Code.
And Breach has one inside her, which may explain why she seems to have such power over reality, including the manipulation of space and time, and the creation of pocket dimensions in which the laws of nature don't seem to have a say. Providence and White Knight realized it when she showed the power to travel through time, and that's why they were so anxious of putting their hands on her in the episode when that power was revealed.

Rex is a Doomsday Weapon and the Meta-nanites are his triggers
He wasn't given nanites to save his life but to be groomed into a living mass extinction weapon hence the picture he drew in "Assault on Abyssus".

His giant robot form wasn't a result of him going berserk but the result intended by the nanite developers. The meta-nanites are meant to be put into him and mode-lock in that form in addition to giving him the capabilities to devastate the world.

The first time his memory got wiped was because Cesar and his pals stopped it as the plan was being put into action by triggering the nanite event. The second time was when the surviving scientists tried to restart the plan again without enough of the meta-nanites.

Cesar and Van Kleiss are the only two who know what Rex really is and Cesar is secretly working on a full measure to take care of Rex in case if someone gets it right the third time. This is why he shot at Rex during the crossover episode because if Alpha absorbs either Rex or the Omega nanite it would bring about the goal of the plan.
 * To this troper, it looked like his builds and One-Winged Angel form were drawn from his lost childhood memories. But your theory does intrigue me.

Alpha was the cause of Rex's accident.
Cesar says regarding Alpha in Heroes United: "It gained a consciousness, and wanted a body. But whatever it built burnt out. So when Alpha attempted possessing living things, Alpha had to be eliminated."

What if Alpha tried possessing Rex? He would've come very close to burning poor Rex out before he was saved, but was in critical condition. The only way to save him was with the batch of good nanites, which could heal him. (Perhaps this was arranged specifically by the group that believed in humans controlling the nanites?)

Either way, though, it was Alpha who caused the accident and forced Rex to be given nanites.

Black Knight Is Specifically Capturing EVOS...
...That mean something to Rex. She got. She's probably going to try and use them as bargaining chips.
 * Confirmed, kind of. The summary for "Remote Control" says it's Quarry doing the controlling, but last we heard he was in Providence custody. Either he escaped, or Providence is backing his efforts.
 * Actually, Breach took Quarry to Van Kleiss the last time we saw him. However, Quarry did mention that he got the tech from Ceasar...
 * A) Argh, yes, you're right; B) He called it Cesar's tech (because Cesar invented it), but did he actually say Cesar gave it to him?

An upcoming episode is titled "A Brief History Of Time".
Either Breach or Van Kleiss is back. Possibly/probably both.
 * Confirmed on The Other Wiki. It's Van Kleiss. 

No-Face escaped the Bug Jar.
"Heroes United" had Alpha supposedly absorb the nanites of every EVO in the Bug Jar, but No-Face is a villain who deserves better than being a victim of a Bus Crash. I say that when Alpha stormed the place and started devouring every EVO in sight, No-Face took the opportunity to do what he always wanted from the beginning, and got the hell out of Kiev.
 * Given the show's pattern of using villains in widely-spaced one-off episodes (ZAG-RS, anyone?) this is a distinct possibility.
 * What if he's somehow involved with Providence and the collars (willingly or otherwise)? Mind-controlling EVOs was pretty much his main shtick.

Feakins will be used as the basis of a method to deactivate or nullify all nanites everywhere
And he will have Took a Level In Badass in the interim.

Van Kliess and Black Knight were lovers before the EVO incident
And the product of that? Circe. She's the daughter of the two Big Bads of the series!
 * It's so far Unknown how Van Kliess knew Black Knight so we may have to wait.
 * That's an easy one: They knew each other through the original nanite project (him on the science side, her on the Consortium side). The mystery is what that relationship entailed and what she wants from him now.

Cesar isn't Rexs brother.
He's his father, but he was only about 14 when Rex was born and his parents took Rex so that Cesar could continue his science career. Alpha did call Rex 'brother', just like he called the nanites.
 * E.V.O.s tend to think of each other as brothers. Also, ew.
 * Jossed, see Hermanos

Van Kleiss is faking his insanity and will sabotage the second Nanite Project.
Some of his actions in Target: Consortium definitely gave off this vibe.
 * When he was awoken from stasis, he seemed to be genuinely traumatized. I don't think he's faking it, at least not entirely.

John Scarecrow was right.
When he said that Rex didn't have what it took to weather what was coming, he was right. Rex stopped Six from killing the Consortium, Black Knight, and destroying the Nanite Reactor. He might have doomed the world because he wanted to go back for Nightshadow. At the very least, countless EVOs will suffer that needn't have.
 * Considering the past few WMGs involve episodes that haven't aired yet in the US, allow me to remind everyone of the existence of the spoiler tag.

The Meta-nanites themselves will become the final Big Bad of the series.
They certainly seem sentient in "Target Consortium", and the other A.I.s in this series have proven evil so far. They want to merge with/possess Rex to better complete their programming to "fix" the world.

When Rex loses his memory, his body goes thru a systems reset.
In the flash back in "Rabble" Rex doesn't look much younger then he is now, but in "Promises, promises" When Six finds him, he looks like he should be in elementary school. The Explanation for this? The giant robot form we saw was Rex overloading on nanites, in order to fix this overload, his entire body goes thru a system reset. This means that not only does his memory get wiped, but his body goes back to how it was physically when he first got his nanites. The reason he seems to have aged so fast sense he was found by Six is that after the reset, his body plays an epic game of catch-up in order to match the age he's supposed to be.
 * That actually makes a lot of sense. You get a cookie for making me feel better about the show.
 * if this is true, it could mean good things for Rex's future. If the memory wipes are triggered by an overload, rather than a periodic event, then they can be prevented.

The program that meant only rex could dontrol the ultimate nanite was only recently completed.
Otherwise, why would the Salazars have bothered releasing all the nanites into the world? I think Rexs parents started it, but didn't have time to finish it before the consortium could get it, that's why they set off the nanite event. The work Cesar has been doing recently has been to finish said programing. That's also why he hesitated when he was saying "Our parents- We programed it that way" he did that because he had to ammend it, since he was the one who finished it it was no longer just their parents that programmed it that way

The Pack.

 * Are being rescued by Breach, to start anew (why is Breach doing it... insanity?)
 * Are being tortured by Breach because they abused her (sucks for Biowulf and Skalamander because they sort-of reformed)
 * Are being kept for a movie or sequel series (Duh)
 * Just died (maybe the nanite wave interfered with her powers despite her not being there, collapsing the portal on top of her and her "guests")
 * Fell into a plot hole (if the series never gets picked up)