Beyond Good & Evil (video game)/WMG

All of the Alpha Sections Headquarters and devices were designed by a member of the IRIS Network.
That's why it's possible for Jade to break into all of the Alph Sections' buildings. A member of the IRIS Network (or at least, someone who was against the Alpha Sections) was the one who designed all of the Alpha Section's stuff. They had to do it in a sneaky way, so that the Alpha Aections wouldn't suspect anything, but if you think about it, there was ALWAYS a trick to get past a guarded room. The robots can disable an electric barrier, there are crates everywhere, and holes in the walls for you to hide behind, the "level 5 death rays" only shot you if a guard activates it, etc, etc.
 * Also, the Alpha Sections' outfits are built so that the helmets give then almost ZERO peripheral vision, and their tanks (which is their one weakness) are bright neon green. They could have easily built a light, removable metal case around their air tanks to prevent them from getting hit, of have painted the tanks a different colour.
 * Not to mention the best evidence of all--they're able to mark Jade's map with "probable locations" of the Alphas' damning activities (because they know which places are suited for it) and have all the codes for the security-code doors.

Jade is responsible for Pey'j's illness.
Not a new fan theory, but definitely one of the more prominent ones. Jade's powers over Life Energy were granted to her by the DomZ. When Jade brought him back to life, she grabbed his right hand. Later, in The Stinger, it shows the DomZ spore growing on Pey'j's right hand. Therefore, it seems likely that she is the one responsible. Indeed, all of the people resurrected by her during the end sequence could be infected.
 * A common sub-theory involving this is that she also touched Double H where his spore grew after the Timed Mission, but she never did. She leans down to talk to him after she frees him, but she doesn't touch him.
 * I watched said cutscene yesterday, and it looks like his left paw/hand/whatever to me.
 * Just marathoned the game. It's his left hand both times.

The next game will involve trying to stop an evil scientific corporation from creating horrible monsters.
The plot of the trilogy was planned out from the beginning by the creator, even before the series got cancelled-Un Cancelled. He stated in an interview that the plot of the next game reveals exactly why animals were so important in the first game, and controlling the species--there are, according to him, "hybrids" created by humans for a variety of purposes. While some have taken these "hybrids" to mean the Funny Animal people, I see them as being more of Biological Mashup-type critters. If this is true, and if the second game keeps the themes of "exposing the truth" the first game had, perhaps there is a slightly shady corporation that is conducting horrible genetic experiments, and creating terrible monsters, with which they could possibly use to harm people? ...Only a thought.

Jade was spliced with a DomZ sample retrieved by said evil scientific corporation. Her parents were initially complicit, then got cold feet and tried to cut and run.
Related to the above and carried further. The reasons behind the Funny Animal races and biological assay done in the sidequest is probably pertinent to the particulars of this idea, but the idea that this was being done with Earth-native life lends itself to the possibility that, when a sample of an alien, intelligent lifeform was retrieved (or perhaps the living individual itself, named Shauni), its genetic material was itself found to be compatible enough to eventually be used for a similar project. Jade was the result, and intended to be studied in a lab environment as part of possible preparation for line of alien-terrestrial hybrids, either with human or other chimeric stock.

The fact that Jade's parents were mentioned as having left her with Pey'j under unusual circumstances before disappearing feels like a Chekhov's Gun, and will likely become relevant in the next game. For this WMG, it follows that they worked for said company, most likely in the scientific role, though possibly also contributing their own genetic material, only to develop an attachment to the infant being studied. Unwilling to countenance the continuation of the program, they stole Jade away and, now on the run, dropped her off with a trusted friend before leading their pursuers off on a false trail that may or may not include faking her, and their own deaths. Her fame following the DomZ incident on Hillys is what catalyses the circumstances of the second game, as it leads directly to her discovery.

Alternately, it's all a DomZ plot.

Jade is The Shifter.
She physically resembles Jenny Everywhere. No other reason, really, but this is Wild Mass Guessing.
 * Could explain how she comes back to life after being shot by a huge security laser, etc. :-)

Jade's Ambiguously Brown-ness is the result of her being a "future" ethnicity.
She does have a distinct ethnicity, it's just not one we'd know of on Earth. Human mate selection the weird thing that it is, it's possible that she's a product of some In the Future, Humans Will Be One Race-type scenario. To extend that, Double H is of the same "ethnicity"--they both have an Ambiguously Brown complexion, black hair (OK, HH's is kind of dark brownish black), and green eyes.

K-Bups are made of people.
The Nutripils factory has huge vats of weird red blobs, suspended in a lava-lamp-like fashion; these are actually pre-processed K-bups, made from the people who died during shipment; since the DomZ have no use for kidnappees who are dead on arrival, as it were, the ones who didn't make it are processed into K-bups and sold as vending machines. Jade never figures it out, which is why she keeps eating them.
 * Nope, they're made from cloned cows. We see the tubes under the slaughterhouse.

The plot of Beyond Good & Evil 2 will primarily be to Find the Cure
The Stinger showed that Pey'g has a DomZ spore in his hand. If you remember correctly, Double H was given the last of the serum, so there's none left on Hillys. The desert-like planet shown in the trailers is most likely where the serum was produced.

The reason the Rasta rhinos at Mammago's want pearls is because the pearls are drugs.
It just makes so much sense! They're the black market, after all, so of course they'd be involved with narcotics somehow. It also explains why Hal, the one with the hat and dreads, acts stoned. It's because he is. They take the pearls, grind them up, put them into a special pipe, and smoke them. The reason why everything gets all weird is because Jade spends too much time at the garage and gets a contact high. There, now everything makes sense.

Pey'j got Jade the library job, which unintentionally lead to her being recruited by IRIS

 * Yoa says something about Pey'j if you talk to her early in the game. The offer of the library job to collect pictures of a speciman of every living thing on the planet comes just when Jade needs money the most. Did Pey'j use his position with IRIS to get Jade that job and Yoa overheard?
 * Similarly, Pey'j is dismayed about the job on Black Island. He does what he can to dissuade Jade first from taking it, then from going to IRIS. As head of IRIS he probably knows it's to recruit Jade. Did getting Jade the library job lead to this unintended consequence?
 * The animal photography job seems to be a public offer, and I don' see how it had led to Jade joining the IRIS Network (in the game it's just a source of money and pearls). It was first mentioned by Secundo, and Pey'j was skeptical about it. (The Black Isle mission was intended to bring Jade to the IRIS Network, and - as we learn - it was Peepers' idea.)

The Metroid universe is the future of the Beyond Good and Evil universe.
(Cross-posted from the Metroid page.)

The DomZ (BGE) have demonstrated the ability not only to steal "Life Energy" and perpetuate themselves using it, but to use that ability to create reconstructions of those whom they deplete--up to and including armor. They also seem to store their energy in the Pearls. Perhaps the "Pearls" are, in actuality, shell-like casings they build up in order to protect their true soft, inner forms--this is not unlike what some real-world creatures do, in particular, a sea organism called Syringammina fragilissima, a giant protozoan. Now, after the defeat of their Priest and loss of their primary life force source (I.E., Shauni), they lost the ability to maintain these bodies--but they could hold forms long enough to return to their home planet, not yet discovered by humans. There, they reverted to their true bodies--gelatinous, levitating creatures--and their old way of feeding, directly consuming genetic material and life from their hosts as parasites.

Meanwhile, the threat of the Alpha Sections gone, the IRIS network turned to a new social conflict: Fantastic Racism in certain portions of the galaxy between Humans and Hybrids. Sadly, they could not stop it. But IRIS was able to help certain groups of Hybrids escape, and Jade loaned them a portion of her powers to help protect them until they could restablish new communities in secluded portions of the universe. The bird-based Hybrids went in one direction, the reptillian hybrids in another, the moth-based ones still another, etc. The different populations each used the gift in different ways. The bird-peoples used it to help them make their chosen world livable for them--but it was still too harsh for most unaltered humans. They began to call themselves the Chosen. In their spare time, they started tinkering with some leftover Alpha and Hillyan armor they had lying around, and built much improved, full-body Powered Armor they could use to defend themselves with.

The reptillian people did much the same, making a harsh planet safe for them alone, but unlike the Chosen, who were happy to live unnoticed, they vowed revenge on the humans and started building up vast stockpile of weapons. They couldn't figure out a use for their gift initially (which Jade was really starting to regret giving them), so they just sort of left it lying around. It wasn't until a group of scientists--geneticially tinkering with a relatively benign pterodactyl-like creature they found one a planet somewhere--took a look at said creature's potentially fierce physical body and realized that the only thing stopping it from becoming, well, unstoppable was a killer instict and a way to keep on going even if it got knocked down. So they invested the Shauni power into the creature and trained it, tweaking its brain to making it intelligent, and continuously growing (so long as its life energy was fed). The result: A nearly-unstoppable killing monstrosity with the ability to regenerate from almost anything, not to mention a vicious inner energy. However, like the original DomZ, he needed to feed on flesh in order to keep his inner power source running. They dubbed it Ridley.

Meanwhile, time had corrupted the name of the avian people into "Chozo," and they were out roaming the cosmos one day (as you do) when they stumbled upon the homeworld of the DomZ. Knowledge of their kind had long ago passed out of Chozo culture, and anyway, there was no one left alive who would have seen them in their original state. They called them the "X", because they had no idea what these strange parasites were--but when one of them suddenly attacked, the life-moving power was frightfully reminescent to them of the darker side of the Gift. They still knew the Gift existed, but they had not done anything with it in a long while. Now, their culture had a legend about how a creature with the power to consume life had been defeated by a warrior who was a limitless fountain of it. Their Gift was supposedly from that warrior, so they decided to use the last of it and incorporate it into a warrior to drive aside the X. Unfortunately, removed from the heart of that warrior, the creature, driven by that life power, was as thirsty and bottomless as the X itself--it destroyed them, but anything else it happened upon as well. Reluctant to have used up their culture's treasured Gift, they abandoned the Metroids and X to one another. Until, of course, the former reptillians--now the Space Pirates--happened upon them...

Luckily, there were those around who knew what the X truly were and what fueled the Metroids. The IRIS network still exists--in particular, because the original members are still alive, rendered immortal by the powers of Shauni. They've pushed and manipulated things behind the scenes for a while, such as helping build the DomZ Sarcophagus-inspired stasis pods for the former moth people (now the Luminoth), but they resisted temptation to directly meddle until it looked like the DomZ/X might break out into the universe again. (Well, OK, they tried to put a stop to Ridley too, but he seemed to be "another Shauni" in that not even Jade seemed able to stop him from regenerating eventually.) Then, they began to work together to create one more Gift--the power to create one more Shauni. One of them, posing as a scientists, posed the idea of the Metroid vaccine for the X--which they imbued with the last Gift. More than part-Metroid, Samus Aran became a new Shauni--ready to take up the mantle in the fight against the DomZ-X.

Oh, and we feel like we should mention--there was one more group of Hybrids that got a Gift. Not only were they eventually vengeful, but greedy too. They tried to use the powers of the Gift to farm Pearls. However, the Gift and the DomZ-traces mingled with the pearls, and created a horrible, spreading crystalline virus. Not only did it destroy them, but the stuff kept growing and spreading until it penetrated the very heart of their planet. Nobody heard from them for centuries, until the thing known as Phazon started cropping up all over the galaxy...

Yoa is a remnant of Toy'l, a cut character from the game's original scenario.
In the original plans for the game (see the What Could Have Been section on the main page), Jade had a third partner character named Toy'l. Toy'l was of an "unknown race," but he was revealed to be a "true" DomZ--the invading people were actually called the Nazh, using the DomZ as a scapegoat. Toy'l's appearance is never described, only that he looks unusual and has psychic powers. Yoa is a bright blue girl who speaks a language very similar to that of the DomZ and chatters about gameplay elements before they actually happen. Of course, since the DomZ are unquestionably evil in the final game, she is, of course, one of the repressed Nazh.

Jade isn't human at all, just made to look like and raised like one
Whatever that element of the Domz was used to be before it was taken, it was reshaped into something like a human baby girl with the thought that this would make it more controllable as it grew. Three workers on the project, believing her to be a hybrid of human and Domz, objected to the treatment of a helpless infant strongly enough that they stole her away and wanted to raise her as their own, but were forced to part ways.

Notice her color scheme? Even her lips and fingernails are greenish. She's Ambiguously Brown enough that the melanin in her skin masks the green tint. It doesn't draw much attention because hey, Hillys - blue people aren't terribly noticeable, and anyway her green can be waved away as due to lipstick and nail polish.

Pey'j got Jade the job of photosurveying the Hillyan wildlife.
One of the orphans, who doesn't speak English, who clearly mentions Pey'j and IRIS in the same breath when Jade says she's got a new job. Did she overhear Pey'j giving instructions to IRIS? Instructions that directly or indirectly led to their recruiting Jade? Pey'j didn't react well to the job offer from Mr. DeCastellac. Unintended consequences for Pey'j.
 * No, as above - again, you are confusing the two missions together. The animal photography mission seems to be a public offer, unrelated to IRIS Network. Mr. de Castellac's mission was indeed aimed at getting Jade into the IRIS Network, but this is clearly said to be Peepers' idea.

Beyond Good and Evil 2 is the new Duke Nukem Forever.
As in, not gonna happen for like 13 years.
 * Proably not though, since it not overly hyped as Duke Nuke Forever, and it really haven't been through Development hell yet.

Jade would have tried to betray the IRIS-network if she hadn't found any evidence
Would make sense since in the beginning of the game the biggest concern she has is to make sure that the kids are safe, and for that she need money because otherwise she can't pay the electrical bill and then they would have no shields. So think back at the first mission when you are on your way to Black Isle you get mail from the Hilliyan army where they ask for information about the IRIS-network and any information is greatly rewarded. So presume that she is successful in her test missions, and then finds the IRIS den, goes on the next mission but she doesn't find anything and she draws the conclusion that the IRIS-network are just some group of thugs trying to get control over the planet. So next things she is reminded by message for army and next thing to happen is that IRIS den is stormed with Alpha soldiers and all IRIS member's are taken prisoner and sent to the moon.

Hillyis is Hyrule in the future
A planet consisting mostly of water with few islands, where the most common means of transportation is hovercrafts and/or flying. This is to be following the time after Legend of Zelda - windwaker, all of Hyrule is drowned, and all left is just some islands. Not to say that I found the two sound very similar and the game play to be that too. Come one true to say that loyal Hillyians and Hylians doesn't sound alike.

The pearls and are filled with eternal life energy
The main reason why the Dom Z and the Alpha section is kidnapping people is so that they can suck people dry clean of life energy. But for some reason the Alpha section is also robbing the people of their pearls. Why? So they can shop at the mamago's garage? No, because they are filled with unlimited life energy. Some Dom Z bosses have pearl in their cores and the light they give out is similar to Jades in the ending when she revives everybody. But of course only one Dom Z at a time can use a pearl for life energy, that is why less significant Dom Z enemies don't drop pearls when they die. So the Dom Z and the Alpha section have three objectives, kidnap and suck pepople dry of life, steal pearls for unlimited life energy to their superiors, and find Jade/Shauni their old sources of life.

The Mamago's guys are saving up a fortune
Why do they only accept pearls as currents(I know black market)? During war time they do business with doesn't seem that important, heck a shark even uses it as a lucky charm. But after the war, they have the biggest collection of pearls in all of Hillyis (more than half). Then they sell them for a "prize".
 * "You have collected all the pearls on the planet" is a shorthand for "all the pearls that can be found in this game". (Or would you think that only 56 species of animals live on Hillys?

The Domz Priest will reappear in the sequel
About halfway through the game, a new, different Domz Priest will appear as a Degraded Boss. The Final Boss will eventually be the Domz God they worship.