Metroid is a series that tends to leave the story and details for personal interpretation, but as we found out with the Prime subseries, sometimes this can get out of hand, creating way too many unexplained plot holes and weakening the games. In light of this, I was thinking in a way that I could make everything make sense and work coherently across the 3 main Prime games, and I came up with the following theory that explains several plot holes of the Prime sub-series. But first, I must make it very clear that this is only a possible explanation that simply cleverly puts everything together and in sync; it may have its downs or mistakes so bare with me. Also, there are four conditions that need to be true for this theory to work:

1. Metroid Prime did not come with the Leviathan that struck Tallon IV, but was instead a normal Tallon Metroid that was abducted by the Leviathan and mutated to become Metroid Prime and serve as its guardian.
2. All Phazon is interconnected somehow. This can be seen at the end of Metroid Prime 3: Corruption when once the origin of Phazon, Phaaze, was destroyed, all Phazon disappeared too. I won’t go into detail as to how it is interconnected because there is really no way to know, perhaps there’s a metaphysical explanation, but that’s already too far fetched.
3. Given the fact that all Phazon is interconnected, Dark Samus can materialize wherever there is enough Phazon. This is also visible both in MP2 and in MP3. Every time Samus defeated a Dark Samus in MP2, that Dark Samus died, it disappeared, but because all Phazon is interconnected, that was only an Echo of Dark Samus, so she would simply reabsorb more Phazon and materialize from the latter into a new Dark Samus.
4. Phaaze is the core of all Phazon, destroying it would destroy all Phazon. This is pretty much the same as Point 2. Phaaze was stated to be the center of all Phazon, and it has been stated that its destruction really did make all Phazon disappear.

If we consider those 4 conditions as true facts, then this theory can work.

During Metroid Prime, Samus confronted and killed Metroid Prime, and consequently Dark Samus is born. Dark Samus acquires an advanced level of sentience, so she’s not just a rabid Metroid anymore, she now thinks. It is also a fact that she needs Phazon in order to survive, as well as to grow in strength.

Now, after their terrible defeat in Tallon IV, the Space Pirates, with high hopes after discovering the incredible characteristics of Phazon, are greeted with the nice surprise of another planet with high levels of Phazon in it: Aether. Another Leviathan had struck Aether some 50 cycles (I think I read this number in some scans, it may be wrong though, but it’s not important) before Samus’s arrival at the planet in MP2, and the war among the Luminoth and their dark, Phazon-induced counterparts, the Ing, had long been going, in fact it was already ending in favor of the Ing. The pirates take advantage of the pathetic state of the planet to harvest whatever Phazon they could get from their bold incursions into the dark dimension of Dark Aether, but they are not alone.

Dark Samus, seeking for Phazon to survive and strengthen, immediately feels the presence of large amounts of Phazon in Aether and goes there. How? Well, either by flying through space (unlikely), or as I’ve said in the aforementioned conditions, she travels through Phazon using its feature of interconnection. By the time she arrives at Aether and begins attacking the Pirates to steal the Phazon they had obtained, Samus makes her appearance and begins to attack the Pirates and Ing alike. Dark Samus identifies her as a threat and attacks her as well, and this is when we can see a crucial aspect of Dark Samus: her Echoes, also addressed in the conditions.

All the fights against Dark Samus in MP2 were actually separate, independent Echoes (clones) of the first one. That explains why they can’t die, and makes sense with the game’s title. We can also see these same Echoes, only weaker, during the final fight against her in MP3. This shows how powerful Dark Samus has become by the time MP2 takes place, and that she has pretty much become invincible as long as Phaaze and Phazon, still exist.

But let’s not forget that Dark Samus is still basically a Metroid, Metroid Prime, and as such, it is her obligation to reproduce. But she’s also part of Phaaze given that she’s made up of Phazon, so she is irreversibly bound to Phaaze and whatever its sentience implies. Keep that in mind.

After the event on Aether and after Samus destroys its Leviathan by sucking up all of Dark Aether’s energy, she leaves Aether for the Luminoth to recover. The Galactic Federation also returns to Aether (this appears in several scans of MP3). They make an inspection of the Pirates’ bases and find the ever-present Phazon left by them there (also indicated in MP3′s scans/storyline).

Samus had weakened Dark Samus heavily, but it is very clear that she is able to materialize in outer space at the end of MP2, so we can see her durability and invincibility working out. The pirates, determined to recover whatever Phazon was left in Aether, make a small attack and are able to take some back to their Homeworld (again, it’s in the scans of MP3).

Remember the starting scene of MP3? All those Phazon canisters that blow up and Dark Samus appearing from one of them? Well, scans from the game speak about that incident. Those canisters held the Phazon that the pirates had taken from Aether, the same Phazon that Dark Samus used to recover and pop out from. It is now Dark Samus’s mission to kill Samus, for she poses a threat for Phazon. She is also able to subdue the pirates (this is all between Prime 2 and Prime 3). She uses them and their technology to steal the Aurora Unit from the Valhalla. Dark Samus needs Phazon, and she knows that what she’s got from the raid of Aether isn’t enough so, empowered, she’s finally able to track down the source of all Phazon, Phaaze, and goes there. How? By the same way she appeared inside the pirates’ Phazon canisters, Phazon’s interconnectivity.

She becomes incredibly powerful because of all the available Phazon, and applies this power into finally controlling the complete pirate Armada once she returns to the Pirate Homeworld. Using a Leviathan, she shows the corrupted and fearful pirates the way to Phaaze (also in scans), and they use this almost infinite supply of Phazon to enhance their ships, weapons, and armor. This is also when she installs the A.U. into Phaaze’s core (I’m guessing it was connected to the core because it is the most logical way for everything to explode as it did). Dark Samus also fulfills her obligations with her Metroid kin by taking Metroids from the Pirate Homeworld, which the Pirates had from Aether and Tallon IV, and takes them to Phaaze, where they eventually become Metroid Primes, thus explaining the mysterious exoskeleton that Samus saw in the Infant Leviathan’s room.

Now it all appeared set for Universal domination. Dark Samus had controlled the Space Pirates, had created more Metroid Primes like herself (ish), and had taken the reigns of the source of all Phazon in the Universe, the center of everything Phazon-related and the ultimate creator, to which everything made of Phazon and all Phazon in the cosmos is connected to, somehow. Only one thing remained to assure Dark Samus’ indisputable success: Samus and the less important Galactic Federation. And so she decided to take on them both, by sending Leviathans to important Federation planets and by corrupting Samus with Phazon (oh, the irony), also taking down any other bounty hunter that could pose a threat.

But of course we all know Samus can’t die, ever, so she survived the Phazon corruption because of the technology the Galactic Federation had been developing since their discovery of Phazon in Aether: the P.E.D. suit. With that and her total kickassery, Samus blew up the Leviathans Dark Samus had created to spread Phazon all around, and then went to Phaaze, blew it up, destroying the central pillar of Phazon and eradicating Phazon everywhere. This was also the only way Dark Samus would definitively die, since as long as there was Phazon out there, she would be able to regenerate, so if there is no Phazon, her invincibility is gone.

Now, that mysterious ship at the end of Corruption is a completely different plot hole, and as far as my knowledge goes, there really is no way to explain it with given facts as of yet.

The creature in question can be found in Metroid Prime, in the Phendrana Drifts. The room is the space pirates’ Research Lab Aether. In the center of the room is a tall containment tube, with a strange specimen in it. When you first reach this room, the specimen can be seen quite clearly, though it’s difficult to get a good view of the creature due to its positioning in the tank. Later in the game, after acquiring the thermal visor, the lights in the room go out, making it impossible to see into the tank. The specimen can still be seen using the X-ray visor, or enough light can be generated with the plasma and wave beams to see into the tank. It does not appear clearly with the thermal visor, making it apparently dead or in a state of cooled hibernation.

This mystery creature is not identified by any of the scans in the room, it cannot itself be scanned, and there are no known references to it in the game. The predominant theory to this point was that the creature was a heavily mutated parasite, produced from the same family as the plated parasite and the parasite queen. However, we believe that the creature is in fact a gamma metroid. Both theories are valid, both have supporting evidence, and neither is definite.

There are many reasons that this strange creature was believed to be from the parasite family. First of all, the skin of the creature looks very similar to that of the parasite queen. It’s a very strong resemblance, and in a game with graphics like Prime’s, that can count for a lot. Furthermore, the mouth structure on the creature resembles the log book illustrations of the parasite queen’s jowls. And since we know very clearly that the pirates were experimenting with the parasites, it is reasonable to believe that this creature is merely a parasite mutation. However, there are two problems with this creature. First, it has no legs. Since there are no known species in the parasite family which can fly/levitate, it is unlikely that this creature would be able to move if it were a mutated parasite. Since the creature is not active(presumably dead), it is possible that the legs had fallen or been cut off, but this is pushing things. The second problem with the creature can be seen on its stomach: the creature has a strange nucleus-like structure on its stomach. There is no such bodily structure that can be seen in the parasite family, or on any of the other creatures which are native to Tallon IV.

As with the parasite family, there are reasons to believe that the unidentified creature is actually a metroid. The most convincing detail is the strange nucleus-like structure on the creature’s stomach. While it is unlike anything seen on any life form from Tallon IV, it is very similar to the main body of a larva metroid. And as metroids evolve, the nuclei moves to the stomach. With the right lighting, you can see a clear membrane outside the nucleus structure.

As of now the creature takes a split path; either it is a parasite experimented on by pirates, or it is a Metroid. There are a few more subtle hints in the room that imply that the creature is the latter. Most prominent of them is the inclusion of two ‘glitched’ metroids on the lower level. These can be found any time you go to the room, as well as the first trip. If you recall, Research Lab Aether was the first area in Metroid Prime that Samus encounters metroids. The first one is scanned and behaves typically, but there are two metroids on the lower level you can fight by attacking their tanks.

If you attack the tanks the metroids can be scanned to reveal a non logbook record that states: “This High Energy Lifeform is a Metroid: Alpha Type”. This was either a working prototype that never got finished, or a glitch, though the likelihood of it being a glitch is low as Retro knew that Alphas weren’t included in any games prior to Metroid II: Return Of Samus. What is far more likely is that this was a hint from Retro to delve further into this room. This led to the discovery of the creature in the tube in the middle of the room. Scans on the lower level tank reveal it to be a failure, albeit as a Pirate test, but was there another factor that made this fail? Further scans located near the tank but higher up mention metroids vulnerability to cold, but one in particular once again stands out. The scan mentions that metroids should be subdued with ice, perhaps more shocking is that it mentions even metroids that appear to be dead should be included in this protocol as well.

In Metroid II: ROS the evolved metroids exhibit a trait that no other metroids in the series have, not even the game prior to it. The metroids appear to stagnate in one spot or location, completely immobile, almost docile until they spot prey in the vicinity and then spring to life and attack. This is likely due to the games engine, but it provides sufficient evidence to make such a claim, because it did happen, regardless of limits in programming. The scan above could be applied to this behavioral trait as it seems that there must have been a reason for this protocol to be established. A live, but stagnate metroid would fit the bill.

All in all Research Lab Aether holds a good deal of significance because it is a room that contains some powerful foreshadowing. The Alpha scans foreshadow Metroid II and the room name itself foreshadows the name of the planet in (Dark) Echoes. It wouldn’t be a stretch to think that Retro Studios included an evolved from in here as well. Until confirmation from Retro or Nintendo, this creature will continue to be an enigma. The Secret Evolution.

You can view the older video here.

This post was a collaborative effort by Jayon andCannon.

Update for Clarification:
The Metroid does not turn into an alpha after sucking on a pirate, it just gets larger, what you see is just a scan that says the metroid is an alpha. The actual evolved “Metroid” is inside the tube and can be seen in the X-Ray pics and videos.

Update 2 Oct-2009:
Added a higher quality and more comprehensive video.

Any Metroid fan is familiar with the space dragon Ridley: Space Pirate general, killer of Virginia Aran, and the last survivor of his race. Ridley is both a loved and hated member of the Metroid universe. He is one of Samus’s fiercest enemies, and has appeared in five of the series’ most popular games. However, how is this possible? How does Samus wind up facing the same enemy time and time again, despite having killed him in numerous previous encounters? We intend to find out.

The first battle with Ridley in the Metroid timeline is on Samus’s original mission to Zebes in Metroid / Metroid: Zero Mission. This battle occurred in a lower section of the pirate base known simply as ‘Ridley,’ an area similar to Norfair in its high temperatures and lava pits. When the battle is over, Ridley appears to spontaneously explode, leaving behind no traceable corpse. However, this is a gaming convention; it’s far more likely that Ridley would have left a corpse, or possibly even survived and escaped (though still suffering from fatal wounds). The latter is possible since, as a space dragon, Ridley can survive in the lava of Zebes which Samus (at the time) could not pass through. Thus he could have dropped into the magma at the bottom of the chamber and either remained there or escaped when Samus left the room. He could have easily survived long enough for the space pirates to find him, especially since they likely knew of his defeat (it was required to open the passage to Tourian).

Immediately after the events of Metroid / Metroid: Zero Mission, the space pirates began to reconstruct the body of Ridley. Since he was so badly wounded, it would have been impossible for his organic body to properly recover. Thus, the pirates undertook an ambitious project to both save their powerful general and to increase his already vast fighting skills. They rebuilt his body with cybernetic enhancements, giving him mechanical limbs and life support systems. In the process, he was also given armor, mechanical weapons, and other equipment. The great space dragon was reborn as Meta-Ridley.

Upon encountering Meta-Ridley, Samus (of course) defeats him. However, we do not see Meta-Ridley die; instead, he is shot by a number of Chozo statues and pushed off an adjoining cliff. He’s seen falling into the mist below; however, is not seen hitting the ground, and certainly not seen dead. While the fall would be more than enough to kill any human (or most other creatures of the Metroid universe), a space dragon could easily survive the impact. It’s not only plausible to believe that Ridley survived the fall, but that he would have been able to walk away from the impact.

After Metroid Prime, Ridley takes a small leave of absence in Hunters and Echoes. He is likely recovering from his last fight with Samus; depending on his condition after the fight, the space pirates may have found him unconscious at the bottom of the cliff, or he may have made contact with them himself. Regardless, Ridley is fully repaired by the events of Metroid Prime 3: Corruption, and his restored body is further upgraded with Phazon.

When Samus once again encounters Meta-Ridley, she manages to defeat him despite the unusual circumstances (falling through a generator shaft at the time). However, we again do not see Ridley die; instead, Samus is pulled from the shaft while Ridley continues to fall to an unknown end. Of course, since Ridley suffers no structural damage during the battle, it is entirely possible for him to fly out of the shaft and escape (especially considering the maneuverability he possesses in the 2-D games). Once he left Norion, Ridley made his way back to the pirate homeworld where he became the guardian of the planet’s leviathan.

Ridley is encountered again in Metroid Prime 3, this time as the further improved Omega Ridley. At this point, he has been further upgraded with more armor and large amounts of phazon. But unlike his former two defeats in the 3-D Metroid world, Ridley does not seem to survive this encounter with Samus; instead, he explodes much as he did in Metroid / Metroid: Zero Mission. However, this death is believed to be literal, since 1) the graphical style of the 3-D Metroid games makes it much less likely that Ridley’s death was a simple convention, and 2) his body would be much more volatile due to the large amounts of phazon (and other chemicals) contained within it. It seems that when Omega Ridley was defeated, it was the true end of the great Ridley.

Nevertheless, the pirate general is encountered again. After Samus eradicates the metroid species, Ridley appears to steal the final Metroid for the pirates. How did he survive the catastrophic events of Corruption? My belief is that he did not. The Ridley faced in Super Metroid is, in fact, a clone.

A Ridley clone is not unreasonable. The presence of the Metroid clones at the end of Metroid Fusion makes it clear that technology existed which could produce an organism from a simple DNA sample. Considering his immense combat abilities, it is quite likely that the pirates would have kept a sample of Ridley’s DNA in case he ever was killed. After Corruption, the pirates had a short time of recovery while Samus was busy on SR388. It is in this time that the Zebes base was rebuilt, and I believe that it was also the time in which the Ridley clone was raised. This hypothesis is further strengthened by a look at the two 2-D Ridley encounters (discounting the original Metroid). In Zero Mission, Ridley was fully grown, and stood nearly three times the height of Samus. In Super Metroid, Ridley would have been fairly young; as such, he would have been smaller. The game supports thins: the Super Metroid Ridley stands only about twice as tall as Samus, or only about 2/3 as tall as his predecessor. It is unknown if this clone carries the memories of his previous life or not; however, it is quite clear that this Ridley is a clone.

As in her previous mission to Zebes, Samus encounters Ridley and defeats him. However, this time his death appears to be absolute; while it is possible that Ridley did survive or escape as in the original Metroid, the likelihood of him surviving beyond the end of the game is minute. Zebes explodes after Mother Brain is killed, taking all those on the planet (including Ridley) into oblivion. This is believed to be the final death of the great Ridley.