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The Metroid Prime husks on Phaaze are from the Metroids that Dark Samus brought to the planet.
Due to a ridiculous number of Metroids in Phaaze, it's possible that some of the Metroids heavily mutated into a Prime, as you can see some husks around the Genesis Chamber. There has been a decent amount of time for Dark Samus to send Metroids to Phaaze

Phaaze being destroyed isn't the end of Phazon shenanigans.
There could still be other planets corrupted by Phaaze in different systems - the Leviathan Seeds could create wormholes, after all. Plus there are still lingering Phaazoids, which are exceedingly difficult to destroy without Phazon-derived weaponry. Enough said. Fridge Horror, anyone?

Why Samus was able to resist Phazon corruption
It's a plot point that Samus and the other hunters (Rundas, Ghor, and Gandrayda) become corrupted with Phazon after their encounter with Dark Samus in Norion. We know that after being outfitted with the PED powered by their own phazon, all the hunters quickly go bonkers and become enslaved by Dark Samus and, by extension, Phaaze itself. But why not Samus? How is Samus able to resist? Some will say that it's all willpower and her being the main character, but there might actually be another explanation: Samus has already developed a certain level of resistance to Phazon.

Even when her Corruption becomes critical near the end of the game, Samus remains herself. While she is at risk of being taken over by the Phazon at all times, she's able to fight it off. Why, you ask? Because Samus has already been Corrupted before. On Tallon IV, Samus became infected with Phazon when she defeated the Omega Pirate, giving her the Phazon Suit. It's worth noting that said suit isn't an external upgrade, it's just her suit getting overloaded with Phazon. Since Samus and her suit share such a close bond as to almost be one, we can assume her organic components were also infected with said Phazon. Since Samus is basically a mute most of the time and given how we can assume the timespan during which Metroid Prime occurs, we have no way of knowing if the Phazon Suit had any negative side effects on her mind. Perhaps she had it for such a brief time these effects never manifested. When Metroid Prime is defeated, it sucks out the Phazon and reverts Samus to her Gravity Suit. Considering how the biohazard scan says Samus is clean in Prime 3, we can assume that she had all the Phazon sucked out of her during this event. In short, she was temporarily corrupted, but then cleaned. This means her body (which incidentally, is genetically modified by the Chozo and is flat out superhuman) likely developed a certain level of resistance to the negative effects of Phazon.

Omega Ridley was a Phazon copy of the original Ridley
Omega Ridley was the equivalent of Dark Samus: Meta Ridley's Phazon-mechanical shell, separated from his body and given sentience. That explains why he explodes at the end of the battle, but reappears in Super totally regenerated.
  • Ridley still has some mechanical enhancements when he returns in Samus Returns as Proteus Ridley, so it's unlikely that Omega Ridley is made of that same mechanical shell. But it is still possible that Omega Ridley is a Phazon-powered copy.

The ship seen in the 100% ending is Dark Samus
Every 100% ending involves Dark Samus in a way(In Metroid Prime's 100% ending, Metroid Prime was revived as Dark Samus. In Metroid Prime 2, it has Dark Samus reforming), so Prime 3's ending clearly involves Dark Samus (Now known as Dark Gunship) being revived as a space ship and going after Samus for revenge.
  • Given that Dark Samus was pretty much destroyed in a huge Phazon-explosion by the end of the game, and knowing that Dark Samus can absorb Phazon and grow stronger, this seems frighteningly likely, especially if Dark Samus now has whatever was needed for Phazon to exist. In other words, Dark Samus is now a monstrous being the same size as Samus, with the power of a planet's worth of raw energy. The universe is doomed, if that's true.
    • Jossed by word of god, it's Sylux. While it's possible that a Metroid Prime might return, Dark Samus is certainly gone for good.

Rundas was faking his baritone.
Notice how Rundas' voice seems a lot higher and more goblin-y when you fight him on Bryyo? It could be that his species, Phrygisians, naturally have higher voices and he was putting on a deeper voice earlier in order to keep up his badass bounty hunter image. Once he was corrupted, however, he couldn't keep it up anymore either out of the stress of fighting the corruption or Dark Samus' influence ignoring his will. Makes sense given his arrogant cool-guy attitude, but has no real basis in facts.

The Phazon corruption in this game is a metaphor for a drug addiction.
When you first encounter the Phazon troopers, the are portrayed as being super cool, being able to fend off multiple Space Pirates all by themselves, and shortly after that Samus and the other Hunters get infected with Phazon, which can be used in gameplay through Hypermode for a temporary boost in power at the cost of an energy tank. As you progress through the game, the player is subtly encouraged to use this boost progressively more and more by encountering stronger and stronger enemies that also using Hypermode, making them take many more hits to kill, unless you are also using Hypermode. In addition, after defeating every Leviathan Seed boss, Samus' own corruption gets worse and worse, from throwing up after the first one, to her veins in her face turning an unnatural shade of blue after the second ones, to the aforementioned symptoms getting worse after the third and forth Levithan Seed bosses. The Phazon is shown to cause Samus both pain and great distress at multiple points, but the game still encourages the player to use it more and more. And at the end of the game when you first touch down on Phazze, you get blasted with so much Phazon that Samus has to vent all her energy tanks: in other words, inject them all to enter Hyper Mode. The scene is reminiscent of an overdose.

When Phaaze is destroyed it causes everyone that was infected with Phazon to be cured.
This will allow the Chozo Ghosts to move on the afterlife.

The "Project Dread" scan was not a cheeky easter egg, but a planned-out reference to Dread at the time.
The infamous teaser scan on Urtraghus about "Project Dread" was not a throwaway easter egg, but in fact a leftover reference to the original premise of Metroid Dread. Consider that Prime and Fusion released simultaneously in 2002, while Prime 2 and Zero Mission did the same in 2004 - there was a pattern for each 2D game to have a 3D counterpart release simultaneously. Prime 3 and Dread should have continued this pattern by both releasing in 2007, were it not for the E3 2005 leak and Sakamoto getting derailed by the DS's specs which delayed it for so long. The resulting game would have again pitted Samus against Space Pirate tech, possibly on a leftover research station of theirs where this mysterious "Project Dread" ran loose.
  • Jossed. Senior producer Bryan Walker denied the scan was a hint to Dread at all, but merely a coincidence.

Bryyo Ice is an alternate world formed by the Chozo, similar to Light and Dark Aether.
It's never explained what Bryyo Ice is; it can only be reached via a portal and AU 242's messages fail to reach Samus once there, so it can't just be another part of Bryyo's planet. The portal cutscenes bring to mind the light and dark portals in Prime 2, making one wonder if its an alternate world a la Dark Aether. Plus the abundance of Chozo statues in Bryyo Ice, despite lacking them in the rest of Bryyo, posits that it's a place of Chozo creation (or at least dedicated to them). Since we know the Chozo met the Luminoth, it's possible they took some of their interdimensional technology and tried using it on other planets to see the effects. On Bryyo it resulted in Bryyo Ice, which they or the Reptilicus briefly explored.
  • An awesome idea, and not necessarily out of the question, but there actually is an explanation for Bryyo Ice in game. After the war between the two groups of natives the remaining science lords who sided with technology went into hiding until they realized the fallout of the war had set Bryyo on a path of eventual ecological devastation. The only way they could find to avoid this was to tidally lock the planet creating bastions of permanent habitability. Bryyo Ice is simply on the far side of the planet permanently locked facing away from the systems star encased in a thick layer of ice only accessible by portal. It also happens to be where the science lord territories were.
    • It still seems odd that there's so much Chozo architecture in Bryyo Ice compared to the rest of Bryyo. Does this imply that the science lords were closer to the Chozo than the primals? It would make sense.

Admiral Dane is part of the pro-bioweapon faction of the Galactic Federation.

Admiral Dane works closely with the biomechanical Aurora Units, the risky PEDs, and plans out the Leviathan Battleship. He is described as a stern man who will do anything to protect the Federation from its enemies, and rumor has it he was orphaned by marauders as a child. This gives him the motivation to do whatever it takes to secure power, even using less-than-humane sources. Not to mention his old concept art almost makes him look like a villain.


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