The Prime Series Theory

Spoilers for the Prime Subseries follow.

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.