Energy is a type of psychic power. We already know that Chozo have mental powers, in Metroid Prime they foresaw the Phazon coming. We also know that Samus has some Chozo DNA. She uses the psychic powers to power her suit. The tanks are just to store her energy. She would also make her weapons out of psychic energy, clearly there is not enough room for her to have 255 missiles in her suit. This helps her 'Crystal Flash' and 'Concentration' abilities make sense. Also the different types of ammo that she uses in the Prime games also makes sense. She is not used to using those weapons and has a limited amount to use, but can concentrate to fire off some. Also, this is what makes metroids so dangerous, they actually feed on this 'energy'. The manga also mentions a type of energy that the metroid were created to feed off of. That is why they are the only things capable of destroying the X, they actually eat the X. This also explains why Samus is able to replenish her energy by absorbing X, she is eating. -Krazycrismore
One has to wonder, why is Space Pirate tech so easily used or hacked by Samus? Their leader is Mother Brain, a Chozo AI. Samus uses a Chozo battlesuit, so it makes perfect sense she'd be able to readily manipulate tech Mother Brain likely had a hand in.
This troper used to cringe every time Metroids were called "parasites" when they're obviously not, but a quote from Metroid Prime used parasite as a derogatory term, and I realized something. They're called "parasites" because they get under your skin.
From Wikipedia, "parasitism is a non-mutual relationship between organisms where one organism, the parasite, benefits at the expense of the other, the host." A Metroid is as much a parasite as a tick. Except they don't suck blood, they suck life force.
In that case, a Metroid isn't a very good parasite; a parasite which too quickly kills its host gives itself little time in which to benefit from the parasitic relationship. (In real life, this is a limiting factor in the spread of diseases, such as Ebola hemorrhagic fever, which are both extremely virulent and extremely deadly; the latter trait reduces the effect of the former, by killing those it infects so rapidly that they have little opportunity to spread the disease.) In general, the observed behavior of Metroids isn't consistent with parasitism; while they're happy to kill anything they can get hold of, they seem able to go an extended period without feeding at all (e.g. Tourian in the original game, where there are many quite lively Metroids despite there being no evidence of anything on which they might feed), and a true parasite requires a host to provide the environment in which it can survive.
On the other hand, an ability to survive long periods without feeding would be extremely beneficial to an organism engineered to serve as a long-term biological weapon against a target which can be expected both to be absent for long periods, and to turn up without warning when it finally does; such a weapon could be "seeded" in many locations, and left dormant and unmaintained until its target arrived. All of this is consistent with the canon statements regarding why the Chozo created the Metroids. Further, it's stated early in canon that Metroids reproduce parthenogenetically in an environment rich in energy, which makes sense; given that capability, the Chozo would need only seed a few of them in each location, and they'd be able to proliferate as necessary to meet an X threat on any scale. The indiscriminate feeding behavior which makes Metroids such a threat to the galaxy at large could easily have resulted from a mutation during reproduction; such a mutation would be highly adaptive, in that it would enable affected Metroids to access a much broader range of energy sources and therefore reproduce much more rapidly, and the Space Pirates would therefore be more likely to happen upon such a mutant than upon an original-strain Metroid only capable of feeding on X parasites. Presumably there are planets on which remain Chozo-seeded caches of pure-strain Metroids which are harmless to anything that isn't X-infested; that they haven't turned up in canon anywhere is easily explained by the fact that harmless Metroids wouldn't serve Samus very well as adversaries.
It's interesting to consider whether the Metroids in Fusion could've been cloned from pure-strain stock; it's a better explanation for their lack of interest in Samus than the fact that she's been hybridized with Metroid DNA — humans and chimpanzees have much more of their genome in common than Fusion Samus and Metroids do, but that doesn't stop humans and chimpanzees from preying on one another; Samus not being X-infested, on the other hand, would render her both inoffensive to pure-strain Metroids and immune to their X-specific predation, thus neatly explaining why they ignore her in a way that the genetic-commonality hypothesis doesn't.
Comments have been made regarding the titular Metroids and their decreasing relevance giving the series an Artifact Title and how Samus is confused with the creatures. But the Metroids were created by the Chozo, and in their language, Metroid means "ultimate warrior". The title does refer to Samus, the most powerful warrior in the galaxy, who repeatedly slaughters the Metroids.
The original trilogy
From the original Metroid when you Start: When you try moving to the right you'll find that you can't get very far and you must go to the left. BUT Samus is looking directly at the player in the beginning, so... the game is making you move to HER right.
In Super Metroid, you eventually make it into Ridley's lair, which you quickly notice is built into the ruins of a Chozo temple, with several rooms demolished and a number of Chozo statues either buried under rubble or half-destroyed. You might chalk this up to damage from the original game...except the main entrance to Ridley's lair is adorned with an image of Ridley's head, and later you find a secret area with a giant underground statue of Ridley carved into the cavern wall. Thinking back along the Metroid timeline, it finally occurs to you: the Chozo have played a major part in Ridley's multiple near-deaths up to this point in the Metroid series canon. Ridley destroyed whatever sacred portions of that temple survived the original game, and then bastardized whatever was left into a shrine to himself as a giant middle finger to the Chozo race because they never succeeded in actually killing him. And then Samus killed him with her Chozo weapons.
Metroid Prime Trilogy
In the first Prime game, nothing about Thardus makes any kind of scientific sense. Except for how it holds itself together: the power up it drops upon defeat is the Spider Ball, which uses magnetism. Considering all the weird things Phazon is capable of, it's not a stretch to say Phazon ore could be magnetized.
In Metroid Prime 2: Echoes, upon entering the Agon Wastes area, probably one of the first things you'll spot is the funny large structure on top of the main area, with some giant caterpillar statue on its side; scanning this statue will have your data suggest that it may be a warning to travelers. Turns out that the statue represents Amorbis, the game's first real boss. This troper now figures that the "warning" was for the player.
Also in Echoes, the Space Pirate base they are in. There are some things about the base that don't make sense at first glance. For example, we know that the Pirate operation on Aether was a very stealthy operation, so stealthy to the point that the Pirate expeditionary force on the planet was relying on a single transport ship making occasional supply drops for them. It seems impossible that such a major base on Aether could have been constructed with only a token force and one ship. But consider a few things:
Echoes features the Space Pirates utilizing some kind of teleportation technology to move around the planet. Corruption also sees some Pirates warping, but it is explicitly Phazon-based; the teleporting we see in Echoes is that a beam of yellow light appears, and a Pirate emerges from it.
Near the end of the game, once you obtain the Light Suit, Samus can also warp around the planet using beams of yellow light. The log book data indicates she is making use of a Luminoth Portal Network.
There are two Luminoth Keybearer corpses in the Pirate base.
The Dark Beam is found in the base, and it is not a Pirate weapon. It is also kept in a secure, isolated chamber, possibly indicating the Pirates were studying it.
Conclusion: the Space Pirate base on Aether is a Luminoth base that they must have moved into upon making planetfall. With an infrastructure already in place, suddenly the fact they only have a single transport supplying them makes much more sense: it would only need to carry weapons, computers, and other makeshift portable gear instead of the kind of heavy construction equipment necessary to build a base from scratch. After getting themselves situated, they must have discovered the existence of the Luminoth warp network and found a way to breach it.
In Prime 3: Corruption, Phazon seems to have a much lower rate of fatalities than the two games before it. But then, in the first game the space pirates had discovered how to drastically increase the survival rates when using the stuff in project vertigo, which got into Samus's suit, which was then stolen by...who eventually took over the source of...and then it all made sense -Cider
Aurora Unit 313's line at the end of its final transmission, about "darkness coming" sounded like generic gloom and darkness are bad diatribe but thinking about it a little more, who is the game's main antagonist? Dark Samus, who was indeed coming-Indirect Active Transport.
Metroid Prime: Hunters
In Metroid Prime: Hunters, the six enemy hunters each represent a main colour on a colour wheel. Look closely at the oppositely coloured hunters. Blue Sylux is the hunter with the most selfish and malicious intentions (sheer hatred of Samus and the Galactic Federation), while orange Spire is the one with the least (he just wants to find others of his race). Green Weavel is a scarred veteran of the Space Pirates, while red Trace is a youthful Kriken full of hope and promise. Purple Noxus is a member of the very Lawful Good Vhozon race, while yellow Kanden is a mindless psychopath. -Mogotoo
Metroid: Other M
Let's face it: In Metroid: Other M, Samus' Concentration ability makes no sense. I mean, she just stands there for a minute, and suddenly her energy is refilled? It actually makes more sense than you'd think. Let's step back for a moment, and consider what has to happen before it can be used: Your energy has to be at critically low levels, or it won't start charging. So here's the question: At the point where the recharge becomes accessible, what is the player thinking? Odds are, they're scared s—-less. One more hit is all it's going to take to cause a Game Over. Now think about Samus' thoughts on the matter. She may be worried about a Game Over, but not in the video game sense. Her adrenaline is probably spiking like crazy. Now that we've got that taken care of, let's look at what she actually does during Concentration. All she appears to do is bring her Arm Cannon up to her head, but if you pay attention, there's a subtle air of focus as she does it. And that's precisely what's happening: When the player activates Concentration, Samus takes a moment to gather her thoughts so she can focus on the task at hand. How her energy is restored is simple: Once her mind is cleared, she has a ton of excess adrenaline that's going to make it hard to stay focused. So what does her suit do? It converts the adrenaline into energy, then pours it into the shields! -phazonfarmer
Alternate theory: Concentration is Concentration. The game shows that the Power Suit is maintained by force of will. After being hammered on for a while, she needs to step back and restore her focus.
I thought it was manipulation of the Charge Beam ability to draw in energy and use it to fuel the suit. as for why you can't fully recharge in that style, well, the Charge Beam essentially creates a big ball of really painful, explosive energy. It could be that only one or two of Samus's many energy shield tanks can support that type of energy.
I figured that was the case as well. And the part about concentration restoring missiles as well? The diverted energy powers a micro-fabricator.
Another option is that her Concentration is an upgrade of her Crystal Flash from Super; she might just be taking energy from a Power Bomb and converting it to her suit systems and physical stamina. Just cause she isn't authorized to use them doesn't mean she can't use their non-lethal abilities.
Other M was all just a bad dream after Samus ate way too many Baconators the night before. When her dream becomes a nightmare (read: low health), she has to stop and reassert the dream's lucidity.
During Other M, Samus is working with Adam's team, and doesn't use any new abilities until Adam authorizes it. Late in the game, she comes across a broken bridge that she has no means of crossing at the time. What does she do? Rather than wait for orders, she activates a few abilities...one of which is the ScrewAttack. -Matic
"Any objections, Adam?"
She couldn't contact Adam, and she was attempting to follow the Deleter. She didn't hear anything from Adam, so she just decided to go "Screw it" and proceeded to activate her two most awesome functions in the entire Metroid series.
"Screw it" is a very accurate wording there, isn't it?
Fitting in with Other M's "motherhood" theme, I realised the name of the space station, the Bottle Ship, was a reference to a baby's bottle, shape and all. Coupled with the fact that the distress signal sent from the station is called "Baby's Cry" it does its job hammering the theme in one way or another. I do know it also may reference the age old "impossible bottle" relic but considering the rest of the game, it makes sense. -MightyKombat
I never saw the whole 'motherhood' theme in Other M. To me, the whole 'Baby's Cry' thing made since A) it means that the target is currently weak and unable to defend itself and B) VERY attention grabbing. No, I instead saw a huge linked theme with Metroid Fusion, Let's see, both games take place on a space station, containing different 'Sectors' with different simulated environments that have many different creatures within, are connected to each other by a series of elevators, include genetically breeding Metroids in the plot and using them as weapons, having said breeding being done by the Galactic Fedaration, being ordered around by Adam and having your abilities restored, partially at his mercy (Although he's much more reasonable in Other M), and, of course, both games taking place after Super Metroid.
There are people who take issue with Samus' calm attitude as she narrates the story in Other M. But think about it for a few seconds, for pete's sake. She's telling the story at an unspecified time and place, most likely where she can remain calm. In fact, she might actually be telling someone else about this, tying in with Metroid Fusion's ending. Would she gain anything by sounding frantic or worried?
She's definitely telling the story to somebody, or narrating a journal entry. She doesn't sound frantic or worried because it's already in the past to her—she knows how it ends, so what's she got to be frantic or worried about?
Another thing to note is why she seemed more emotionally vulnerable. She's barely had any rest at all between Metroid 2, Super Metroid, and Other M. She lost her 'child' and her home all in one fell swoop. She's been through hell and back and, like a determinator, she went out to keep going when she should have taken some time to get proper rest.
Hell, this even culminates in one controversial point. Ridley who, to us, is merely a Recurring Boss Fight to which we expect, made Samus go into shell shock in Other M. But think about it from Samus position, with the above info in mind. She thinks Ridley is dead and gone, never to bother her again. And yet he reappears, as if emerging from hell itself, illuminated by the magma's glow, completely breaking her facade of toughness and reestablishing Ridley as a being from her nightmares. It takes a near Heroic Sacrifice to make her snap out of it, partially in rage of having someone else seemingly die because she wasn't able to stop Ridley or some other force from killing them.
This makes more sense too if you look back to Metroid Prime: Corruption, back on Norion. When Ridley ambushed her inside, Samus didn't get out of the way but stood thre and shot at him, even though she knew that it wasn't going to do much of anything. Even after the events from the Manga, She still has a little bit of fear left over. Fear is never truly gone, after all.
It makes even more sense when you consider that the writers for Other M did not consider the events of the Prime trilogy when making it. If you ignore Prime, Ridley has only officially died once (Super Metroid) and that was supposed to be Dead for Real. So his resurrection would have looked impossible to her - she saw his body disintegrate in front of her, and how he's attacking? He'd have to be some sort of demon. She also probably didn't figure out the whole "fluffy bird thing = furry lizard = Ridley" thing either, since she looked at the shed skins of them with mild confusion, but no sort of worry.
In Metroid: Fusion, Samus maintains that the X are evil and destroys them to save every race that exists. Adam mentions that the X are gaining intelligence. Eventually, they stop worrying about themselves individually and instead seek to preserve their race by blowing up the station and killing Samus, the only person in the galaxy who can stop them, and the Metroid, the only race that can kill X. No X ever seems to care about anything other than X, however. Fast-forward to the end. Samus plans to destroy the station, the planet the X came from, and the X entirely. The X counter-attack with the only X powerful enough to kill her: SA-X. After she beats SA-X, the X stop attacking her altogether, they don't even try to slow her down on the way to her ship. Then, during the battle between Samus and an Omega Metroid, the SA-X arrives and saves Samus, which allows her to escape. The X are pretty much doomed at this point and so is the Omega Metroid, so if they wanted to take out their enemies, all they had to do was wait. I believe that the act of offering itself as a power-up to Samus could have been three things: 1. Respect and possibly compassion to another race, indicating that the X had evolved beyond total Xenophobia. 2. A way to preserve itself as a legend instead of complete obliteration. 3. Returning Samus' suit as a gesture of courtesy. Samus does not appear to notice this, but I think the X were developing signs of intelligence beyond assimilation or Always Chaotic Evil. Another reason Metroid Fusion is my favorite Metroidvania game. -Ekul
Fourth option: Instinctive, animalistic "use whatever means available (*coughSamuscough*) to destroy the Omega Metroid" reaction, without realizing the whole Colony Drop bit.
The SA-X was trying to steal Samus's ship so that the X could survive. Only no one counted on the Eticoons/Dachora actually doing anything. And most likely, the Omega was holding a much larger "This is a Metroid. KILL IT" sign than Samus was.
A MUCH more reasonable option is that it was trying to kill the thing that was more of a predator to the X. Metroids are an X's only predator, and compared with Samus, who has only partial Metroid DNA, and an overgrown Omega Metroid, what do you think the SA-X would target first?
Possibly all of the above. The X had found a Worthy Opponent in Samus, or at least SA-X did. As she absorbed so many of them, she would act as a depository of DNA for them which may one day be extracted to make more of them. Also, Samus, both as a gene bank and a worthy opponent, was facing off against an enemy she couldn't beat and who the X had personal enmity with. So, the most reasonable solution was to work with the only one capable of killing it.
A depository of DNA is unlikely. The X are the DNA stealers, not the Metroids.
Or better yet, the X saw evidence that Samus was a predator of their predator; having failed to kill an Omega metroid, they chuck the thing that kills Omega metroids, to wit, Samus Aran, at it, after equipping her with the means to do so. If it hadn't been for all X being erased by the colony drop, Samus would presumably have helped them hugely by killing any remaining metroids. Certainly, she had so far...
Also, despite having both Samus' knowledge of how to kill Metroids and the equipment at its disposal to hunt and kill Metroids, the SA-X consistently failed to hunt and kill anything Metroid on its own power. It failed to find and/or kill Samus on multiple occasions, and was even overpowered by her when they finally engaged each other in a one-on-one fight. It was easily overwhelmed by Baby Metroids in the Restricted Area. Those baby Metroids were ejected and destroyed with the SA-X by the station's automated systems, which denies the SA-X even that small victory. The SA-X barely managed to tickle the Omega Metroid before getting taken out in one swat. The only thing left for the SA-X to do towards killing even one freaking Metroid was to give its Ice Beam to the accomplished Metroid hunter so she can kill the Omega Metroid herself.
The moment SA-X came to Samus aid was also the moment her Energy Low alarm sounded. Think about that for a second.
I had my moment a while ago when I played that game. I always assumed that she wanted to eliminate the X because it was her job as a bounty hunter to carry things through. I then realized that, as a bounty hunter, she had no obligation to do so once Adam told her to stay put and wait for the Federation. She disobeyed, but possibly not out of her own humanity. It's possible that the Metroid vaccine in her body had infected her just like the X did, and that she had become part Metroid. Playing through, I noticed that colliding with the Metroids that inhabit the Restricted Section while you try to escape does no damage to you (it just slows your jump). I thought it an example of Mercy Invincibility at first, but realized that those very Metroids may have recognized her as one of their own. It makes more sense when you figure out that the Metroids were designed to fight the X by the Chozo. How do you make a better predator than the Metroids? By combining it with the very thing that wiped them out. The X may have realized this and chose to live on as a part of Samus despite being absorbed harmlessly and turned into "food". The reason the Omega attacks you is nothing less than the fact that it's going to die no matter what, and that it wanted to establish itself as the ultimate predator again by killing Samus first.
Weren't these metroids descendants of the Baby? We don't have much evidence one way or another that metroids possess genetic memory, but we do know that they possess good memory and that while most of them have little metroid sacks, some seem to reproduce by budding (namely fission metroids), which would, presumably, copy memory. We know the reproduction had to be asexual, because the federation only had one metroid at their disposal.
Or it could have been, you know, just a wild animal.
All the above is based on a interesting assumption. That the Omega Metroid wouldn't survive re-entry. Are you willing to bet it won't? Is Samus? Are/is X?
If it survived re-entry, would it survive the planet being blown to chunks?!?
Other M allows for another possible explanation. Both the Omega Metroid in Fusion and the Queen Metroid in Other M were cloned from the baby Metroid in Super. This means that the baby, and, by extention, all of her clones, are potential Queens. Samus also has the same DNA from the same baby Metroid inside of her. Could the Omega be attacking in order to weed out the competition for the position of Queen? -DarkeLourd
You sound like the guys on Wikitroid. But I agree with the very 2nd option: that it was just a wild animal killing everything in sight. FTLOG, Samus was part Metroid, you think it'd not attack her if you know that, but no.
Maybe the Omega was only acting in self-defense. In gameplay it will attack you if left alone, but perhaps, as far as the plot is concerned, Samus shot the Omega first, seeing it as a danger or an obstacle preventing her escape.
Or just competition for the same prey. Predators are territorial already, and the two eat the same thing.
It wasn't until my third playthrough of Fusion that I realized that Adam was a subversion of HAL-9000 of 2001: A Space Odyssey. There's even an "open the doors" line as a Shout-Out! -Duke
Not just that, but the first time that you get a hint that something might be wrong with your new CO is a great homage to 2001 as well. After Samus restores her Plasma beam, Adam starts acting confused, and pauses for a moment, saying 'Wait... Wait a second... More trouble. Hold on.' and isolates a new problem in ARC sector. HAL acts similarly when Dave begins to question him too much, saying 'Just a moment, just a moment.' and isolating a problem with the AE35 unit. Now you have to ask yourself 'How exactly did the Nightmare escape?'
And late in the game, Adam tells you that there are 10 SA-X patrolling the station looking for you. However, this is at the point of the game where you can go anywhere and pick up all the items you missed earlier, and if you do, you don't ever run into any SA-X. Why? Because Adam was lying to Samus and trying to scare her into leaving the ship.
It's easy to say how Nightmare escaped. After Samus activates the security doors level 3 (yellow) and gets the ice missile data, you return to the navigation booth to learn about the emergency in PYR. On the way back Nightmare's shadow can be seen in the background of the large room. So Samus released it.
It does seem plausible that Adam may have had a hand in B.O.X. reappearing, conveniently after Samus unlocks the red hatches without his permission, recovers a couple unanticipated upgrades, and gets a glimpse of unauthorized areas. If nothing else, the way he acts during the conversation when he sends into back into Sector 6 seems fishy.
Metroid Prime 2 takes place on Aether, a planet that is known to be a rogue body. This planet, alongside all others visited in the Prime saga save Hunters, suffered the impact of a Phazon meteor. Because Phaaze supposedly always targets a planet for invasion, you can notice that poor Aether wasn't meant to suffer the impact, it only crossed in the way to an actually targeted planet!! Poor Luminoth race...
Not necessarily; a rogue planet once discovered would be easily characterized in terms of its vector, and such characterization would be necessary if anyone intended to visit it ever again — if you don't know where it's going, how do you expect to find it when you wish to return? Targeting it with a Phazon meteor then becomes an elementary problem in ballistics, such that hitting it on purpose is many orders of magnitude simpler than doing so by accident. (This remains true even when you consider influence from other bodies of significant mass; projecting the last known vector of the rogue planet would lead to any such bodies close enough to exert gravitational influence, and knowing the mass of all bodies involved would allow further extrapolation to find the planet's current position and vector. NASA has done this for decades with interplanetary probes; for the Galactic Federation, or whoever, to do so, would be so utterly trivial that their astrogation equipment would probably do it automatically.)
In Metroid: Fusion, Samus sees her deceased CO, Adam Malkovich, as a mentor to her, and even compares her ship's AI to it. Then Other M rolls around, we meet Adam when he was alive, and he seems a lot more like an uncaring jerk. Some have even theorized that he's a sadist, and compared their relationship to that of an abuser and his victim. This retroactively changes one's interpretation of events in Fusion as well. And since that Adam was Adam's brain, all those times it locks her in the Navigation room and refuses to let her out until she listens to him are somewhat chilling. In Other M, Adam nearly lets Samus die in a fiery area before authorizing her Varia suit. The quote below is from Fusion.
The ending of Metroid Fusion. As the player we know that the BSL and SR388 had to be destroyed, but the Galactic Federation did not. Samus destroyed a research facility and a planet, then fled the scene. In modern day times that would be like blowing up a research lab and a large amount of a park or such. Samus would be seen as some sort of terrorist, and a very dangerous one too. So, if the Metroidverse has any sort of threat come to it, Samus would be on the run from the GF with a large amount of forces after her. So she ends up either on the run for the rest of her life, likely killing lots of GF troopers along the way, turns herself in to be incarcerated and likely executed, or dies fighting against the GF.
Also, there has been no evidence to suggest anything besides Metroid or Samus can defeat X, there is evidence showing that they are the only currently known being that can kill them. This means that the destruction of the BSL and SR388 didn't actually destroy the X, but just left them stranded in space. The GF will investigate the previous site of SR388 and the BSL, and we know that X can go through walls, so once the GF arrives to investigate/search for Samus' path the X will easily be able to board GF ships and become a legitimate threat to the universe. Where will the only person able to stop them be? She will be chased by the GF for what she did at the end of Metroid Fusion. By the time that the GF realizes Samus was correct, it will be far too late as the X will have already become to widespread to stop. Bit of a Downer Ending huh?
Guess you missed the whole scene about the finale in the first place. The self-destruct mechanisms in that laboratory were set to literally vaporize everything within a set radius, and by crashing the station into SR 388, that included the planet itself. X may be resilient, but I didn't see or hear any canonical technobabble stating that it could reconstruct itself from its constituent atoms and/or molecules. Think of it like the MD device from Ender's Game- what's left is just pure matter and energy, completely devoid of life. Samus had just absorbed the final remaining X-core of any significant power (Making the assumption that Adam was lying about multiple SA-X isn't a stretch considering we never saw any other duplicate X-cores.) meaning all that was left were X-based reproductions of the natural fauna of SR388, none of which could survive the vacuum of space, or could reasonably withstand the sort of force that Adam calculated would vaporize the entire planet of SR388. Perhaps if they'd had a suitable host to use as a defense against the shock they might have had a chance, but as it stands it's pretty safe to say the only X left in the galaxy is that within Samus' own body. Well that and wherever else they might have come from to begin with (Metroids as a species were created by the Chozo specifically to combat the X parasites, who had either evolved or arrived on the planet and were quickly destroying the planet's ecosystem).
So you've beaten the Nightmare. It's a deadly beast that obliterated half the ARC sector and flooded part of the rest. Think on it; this horrible cyborgic Mechanical Monster was on this station THE WHOLE TIME. IT WAS ALWAYS THERE. Nightmare could have found you at any time, and there was absolutely nowhere you can hide from him. No chance of survival if you were jumped; he'd kill you.
Also, still about Nightmare, It says a lot about the mental state of the leaers of the GF. I mean, just to design it you need to be disturbed, and the fact it's only ever found on GF ships means they're not just building their own Eldritch Abomination in a box, but they're recreating the monster. And you've been helping to keep these people in charge.
Actually, the Nightmare didn't appear until you opened level 3 security locks, used to contain it. After that, it was released, and you could see its shadow in Sector 5(ARC), and eventually, you had to fight it due to it being infected by the X parasites.
Also, it cries before it loses it's mask. IT KNEW WHAT IT WAS BEING FORCED TO DO. IT WANTED TO DIE.
That relies heavily on it still being the original Nightmare. If you notice, the background of the arena is a giant mass of wires and metal. The Nightmare you were sent after is already long-dead, just like Serris. What you fight is the X-clone in both boss battles.
The real Nightmare isn't even onboard the BSL, unless someone was stupid enough to build two of them. The real Nightmare is on the Bottle Ship in Other M, and is just about as nasty as Nightmare-X. The logical conclusion is that someone entered the room after Samus had slain Nightmare onboard the Bottle Ship (possibly the Deleter), found a piece of biological tissue from the destroyed Nightmare, sneaked it unto a ship and transported it to the BSL-station, where the X Parasites found it and assumed Nightmare's form, all while the computer knew about it (and knowing the Metroidverse, it's not impossible that the BSL could've had a biological AI that might have been infected by the X Parasites as well).
It's likely either the same Nightmare or a second built one. The Nightmare is GONE in the Epilogue of Other M, suggesting the GF removed it after the main incident. And the GF is definitely stupid enough to construct a second one, if not simply rebuild the existing one. The reason it probably was a real Nightmare at first is that the way Adam talks about it in Fusion all but states there was a living, breathing Nightmare on board being researched for military applications. The real nightmare was indeed on the Bottle Ship but it's quite likely the GF brought it to BSL and rebuilt it or used their data on the original to build a second. The Deleter could not have removed it since the Deleter was clearly dead by the final events of the game (All indications was that it was James, who Madeline fed to the Queen Metroid.), plus in the epilogue the entire Nightmare (And Ridley.) were gone, suggesting the GF removed it entirely, not just a sample. As for the BSL station having an organic computer, while possible, it's unlikely. The X had to do things such as MANUALLY overload the boiler, wait patiently for Samus or the SA-X to let them in new areas, manually choke up the reactor silos, and try to kill Samus before she could start the self-destruct. If the computer had been an X host, they could have blown up the whole station without sending an X to the boiler, could have completely unlocked all hatches at the same time and overrun the station before Samus even arrived, shut down power immediately upon Samus' arrival and kept her contained where they could send some powerful combat forms to kill her, and simply halt the destruct sequence. Not to mention we've seen nothing like station systems try to kill Samus except for the security robot, which could have been responding to the X threat at first by trying to kill anything that moved as a simple solution (Later it clearly plays host to X.).
Perhaps one of the more frightening aspects of Metroid: Fusion. Though according to the opening narration death is often pretty much the inevitable conclusion of an X infection, certain events and enemies fought in the game seem to imply that until the host is dead the X can actually control the host and change its cellular makeup until it does die. This may imply that the unwitting X host might be fully aware of what the X is making it do up until the very last moments of its life. It might very well be that an X parasite prefers controlling a host until it dies before assuming a form directly. It also appears that some hosts can survive infection once the X is disrupted, but most hosts, such as the Nightmare or BOX, seem to die horribly if their parasite is disrupted.