Metroid Prime was an original Metroid from SR388 the Chozo brought with them until a Leviathan Seed hit the planet.
In Metroid: Samus Returns, the Chozo Memeories showed the Chozo creating Metroids to fight against the X Parasites until they are all but gone. At least one group would go to Tallon IV with a few Metroids to study the effects of Metroids of other planets, hence a large number of Chozo ruins. However, the Leviathan seed was on-course towards Tallon IV, which would struck the planet while mutating a Metroid beyond recognition until it became a Prime. As a last ditch effort, the Chozo made Artifacts to lock Metroid Prime in the Impact Crater, which would remain until Samus finished her mission on Zebes.
- I like the idea, but as far as the Logbook states the Metroids were introduced to Tallon IV by the Space Pirates, not the Chozo. There likely weren't any Metroids on the planet 50 years ago when the Leviathan hit. It's still possible though for a Space Pirate-brought Metroid to have gotten into the Leviathan, if it became a Phazon Metroid (like from Prime 3) and phased through the lock on the crater to eat the Phazon and evolve.
- But considering the creation of the Metroids happened years before the events of Metroid/Zero Mission, and Samus Returns, there's still a possibility that the Metroids were created 50 years ago, and they were still loyal to the Chozo that went to Tallon IV, but everything went to hell when Phaaze sends a Leviathan seed into the planet, and most of the Metroids lost their loyalty after mutating, and one of them became Prime. The Pirates that went to Tallon IV with the Metroids they had with them may have been unaware of the effects of Phazon on them until they did their experiments.
The Metroid Prime was a Leviathan Guardian.
It states in the infant Leviathan scan in Corruption that once Leviathans reach adolescence, they are launched at other planets inside a Phazon seed. After impact, the Leviathan enthralls and mutates a local predator to guard the core of the seed and then dies naturally, leaving its shell to act as some kind of armor to the core. The Metroid Prime itself couldn't have been a Leviathan, as the meteor struck over 50 years prior. When a Leviathan hit Tallon IV in the first Prime, it corrupted a Metroid as a guardian. After its master died, the Metroid continued feeding on the Phazon and eventually fused with shell/core, thus becoming the source of Phazon on Tallon IV. This explains why there were pieces of shell similar to Metroid Prime's on Phaaze and why the Impact Crater's Phazon was orange (it was created directly through the Metroid Prime, rather than the seed). It also explains why destroying the Metroid Prime destroyed the entire Impact Crater.
- I think that scan was meant to imply that the creature on Tallon IV was an immature Leviathan - you'll notice that the scannable carapace in Corruption is found directly under an infant Leviathan, implying that the infant molted out of its carapace before cocooning itself. Perhaps the Tallon IV creature was the Phazon equivalent of a premature birth, being expelled from Phaaze while the Leviathan within was still embryonic. As a result of it having been "born" so small and weak, it could only corrupt one small area of the planet over a 50-year span, and the Chozo were able to seal it away with minimal difficulty. That may also explain the orange Phazon, too; the Tallon IV creature may have suffered from some congenital defect or birth trauma that made it produce abnormal Phazon in addition to the usual blue stuff.
- I'm more inclined to go with the first idea, that Metroid Prime was a Guardian, a Metroid left behind by the Chozo, ensnared by the Leviathan, and mutated by heavy exposure to Phazon in the core. Its situation is mirrored by the Guardians in Prime 3's three planets - all four are local creatures corrupted to serve the Seed. Prime was just 50 years farther along. As for the scannable carapaces (there were two), I think the ridiculously heavy Phazon radiation on Phaaze had quickly mutated some of the Phazon Metroids there in the same way as Metroid Prime, and Dark Samus (who is Metroid Prime herself, lest we forget) killed them so that they would not be rivals to her power.
- Following this, it would also be safe to assume that if Metroid Prime was the guardian of the Talon IV seed, the Emperor Ing was the guardian of the Aether Seed.
Reconciling the Metroid Prime's location problem
- There's a notorious Plot Hole regarding Metroid Prime (the creature): if it was supposed to be sealed in the Impact Crater due to the Artifact Temple, how did the Pirates capture and experiment on it? Later versions change the text so that the Pirates can only detect what's beyond the barrier, but then how did Metroid Prime get a bunch of mechanical weapons systems, many of which resemble Pirate tech seen earlier in the game? As it turns out, there's some unused Chozo Lore
that indicates a slightly different purpose for the Cipher: rather than being scattered throughout Tallon IV to prevent the seal from being broken, it was already placed in the Artifact Temple, and the Pirates scattering the pieces broke the seal and allowed Phazon to continue spreading throughout the planet. While this doesn't really mesh with the Chozo Lore as presented in the final game, it makes the NA version of events make a great deal more sense. Presumably, in this version of events, Samus would still need to kill Metroid Prime to prevent it from escaping or being unsealed again, while bringing the Cipher back together would isolate the Impact Crater and once again prevent Phazon from spreading, maybe even causing it to die out completely over time.
Reconciling the Red Phazon discrepancy
The mysterious "Red Phazon" found inside the Impact Crater is supposedly a highly-concentrated form that is 86% more mutagenic than the usual blue Phazon. However, in Corruption Samus travels to Phaaze, the source of all Phazon, and only finds blue Phazon there. Surely Phaaze would have the highest-concentrated Phazon in the galaxy, no? There are a couple of possible explanations as to why Red Phazon is only found on Tallon IV:
- Red Phazon is not actually Phazon. Maybe it's a kind of waste, or a derivitive form that is not natural or "healthy" Phazon. In the official guide for Metroid Prime it is simply called radioactive sludge or ooze, implying that it might be something completely different. (The name Red Phazon only ever appears in the Fusion/Prime combo guide; it's never been called that anywhere else).
- Red Phazon was created by the Metroid Prime. The Metroid Prime is described as "the source of Phazon" in the Logbook, which is usually the role of the Leviathan's Phazon Core. It's possible that the Metroid Prime ate the Phazon Core and assimilated its abilities, but because it's a Metroid - a different creature completely - it produced the mutated Red Phazon instead. This is supported by the fact that Fission Metroids spawn out of bubbles in the Red Phazon in the chamber prior.
- But in the fight with the core essence it creates pools of blue Phazon no problem?
- This is supported by What Could Have Been, since apparently Phazon was originally planned to be a byproduct created by Metroids after eating lots of energy. Of course, when you word it like that, it makes it sound like the Impact Crater is actually full of deadly Metroid Prime manure...
- Red Phazon is only found deep underground. While it is true that Samus saw no Red Phazon on Phaaze, she never went completely underground like in the Impact Crater. Sure she reached the Sanctum, but she never entered the chasm below the Sanctum from which Dark Samus and later the Aurora Unit emerged. It's possible that you'd find Red Phazon down there instead - maybe that's why the Aurora Unit has red spots and highlights along its body.
- For those curious, hacking the game's camera to go down there yields nothing but a blue glow.
- Red Phazon was mutated by Tallon IV itself. The Metroid series is no stranger to planets having unique energy, such as the Light of Aether or SR388's Aeion energy. It's possible that Tallon IV's ecosystem somehow synthesized a more powerful mutant Phazon once it began to be corrupted just because it's Tallon IV.
- Red Phazon is unhealthy or "dead" Phazon. We really don't know much about how Phazon works, since it's apparently a mineral but also possesses many organic traits. It's possible that Red Phazon is an unhealthy form of blue Phazon created when the Chozo locked up the Impact Crater, slowing the flow of Phazon and messing with the Leviathan's natural processes.
The reason the Space Jump only lets you do a double jump in this game is because the Tallonian Chozo chose to live a more low-tech life.
"Low tech" is relative (for instance, the Tau in Warhammer 40,000 are considered "low tech" and yet they still have things like spaceships, plasma weapons, and robots), so while the Tallonians might have been living low-tech lives compared to the Zebesians, SR388ers, Elysians, ZDRians, or Chozo on any other planet the species inhabits/inhabited, that doesn't mean that they were going back to the stone age. It's possible that the version of the Space Jump available in this game only lets the player do a double jump because a version that would let the player do infinite jumps would be too "high tech" for the Tallonians' tastes. As for why the Space Jump in 2 and 3 have the same limitation, it's because it's literally the same instance of the item Samus picked up on Tallon IV: In 2 she loses it to the Ing and gets it back from the Jump Guardian, and she starts 3 with it.- In addition, this may explain where the Spin Boost came from: The Chozo on ZDR saw the Tallonians' Space Jump and figured it'd probably work as a sort of "budget" Space Jump (it'd basically be the 2DS to the regular Space Jump's 3DS) or a training tool meant to prepare people for the regular Space Jump (similar to how a pilot might be trained using small, weaponless propeller planes before graduating to larger, possibly weaponized jets, or how a soldier might be trained using .22-caliber semi-auto or bolt-action rifles before graduating to higher-caliber, fully-automatic weapons), so they made their own version of the Tallonian Space Jump and renamed it.
The Space Pirate race in this game is related to the Chozo.
The race of Pirates on Tallon IV and the Orpheon have very similar anatomy to Chozo, especially the Chozo Ghosts: a hunchback, three fingers, three toes (two in front and one in the back), and similar heights. They were posted around Tallon IV for the Phazon but also for the Chozo technology there, but found themselves incompatible with it because of how much genetic engineering they've undergone over the years.