Examining the claims about Metroid Other M's alleged retcons/continuity problems.

CLAIM 1:

"Other M calls Space Pirates "Zebesians" even though Prime 3 shows their Homeworld isn't Zebes"

I truly don't know how this became a misconception, because since Super Metroid the Zebesian Space Pirates have been called "Zebesian". As also noted in Super's manual, "Space Pirates" are not solely comprised of Zebesians but other species like Kihunters as well:

Super Metroid manual page 34.

Metroid Fusion manual page 25.

The reason Zebesians call themselves such is as simple as them making Zebes their home, as allegorized by Yoshio Sakamoto (co-creator/writer/director/producer), it's like those who immigrate to America now call themselves "American":

Metroid: Zero Mission Japanese website FAQ. Translation via Metroid Database.

The Metroid Prime Trilogy art booklet (which was bundled in the Collector's Edition) clarifies the Pirate Homeworld is just "one" of their homeworlds:

Metroid Prime Trilogy booklet page 3.

"First, Dark Samus sends a Leviathan to one of the Space Pirate homeworlds"

Unused logbook entries in Prime 3 would refer to the planet as "Urtraghus":

Via Metroid Fandom wiki.

Though unused content is dubiously canon, the name still survived in the final game in the form of the Urtragian Shriekbats found exclusively on the Pirate Homeworld:

Urtragian Shriekbat logbook entry in Prime 3.

CLAIM 2:

"Other M says Space Pirates would be dumb unintelligent creatures without Mother Brain, if this is the case then they'd not be able to do all they did in the Prime series when Mother Brain wasn't leading them"

In Other M Samus is referring to Zebesians, specifically the artificially created Cyborg Zebesians and is merely speculating based on the fact the illegally operating sect of the Federation were planning to use Cyborg Zebesians as bioweapons, why would "Madeline" fear they could resurrect as the Space Pirates:

"Say that the Zebesians, under Ridley's influence, became super-aggressive... Would that really lead to the resurrection of the Space Pirates? Without a malicious force to lead them down that path, wouldn't they continue to merely follow their instincts, ultimately becoming no more than a swarm of feral creatures?"

Again, Samus is referring to the Zebesians and not all the other forms of Space Pirates seen throughout the series, the Zebesians are just one of the many species that make up the whole of the Space Pirates.

Regardless, the comment about them effectively needing a malicious force to lead them down the path of being the true Space Pirates is consistent with the rest of the series.

Mother Brain led the Zebesians in Metroid & Super, and while they were noted to be a problem on their own, they were never depicted as a "galaxy dominating" level threat, it wasn't until Mother Brain guided them (and through the use of Metroids) were they that powerful.

Beyond the Zebesians we see the other Pirates are also at their strongest when led by others as seen in Prime 1&2 where they are led by an unseen Command/High Command, but they are at their most powerful in the Prime series when led by Dark Samus in Prime 3 where they became a galactic threat once again.

Prime 1&2 shows some of its Pirates as not being the brightest when left to their own devices, such as using Metroids as target practice or pets, which sometimes ended in their deaths:

Via the various scans in the Pirate Base in Agon Wastes in Prime 2.

Some Pirates criticized their own Science Team for attempting to tame Metroids, saying they have "vapor for brains":

Other Pirates were caught using equipment for amusement purposes:

These examples show they are not always the most well organized or smartest group.

The 2002-2003 canon Metroid Manga by Magazine-Z explicitly shows how the Zebesians work best when guided by a greater force, comparing them to worker bees being influenced by a queen bee:

Metroid manga vol. 1, chapter 7, page 5. English translation via Metroid Database 

If Samus's comment about the Cyborg Zebesians even apply to the real Zebesians, then this is just falling in line with what had already been established.

Adding to this, though the Prime series doesn't depict Zebesians, the Pirates seen in Prime 2 are described as "trained to follow orders without question" which is what made them susceptible to Ing possession:

Dark Trooper logbook entry  in Prime 2.

CLAIM 3:

"Other M says Ridley can't lead the Space Pirates even though past games said he's their leader"

Whilst it is true Ridley had been called leader of the Space Pirates, that was only until Mother Brain took control, after that point she became the true leader of the Space Pirates and Ridley became more of a military commander. This misconception stims from the same quote above when Samus says:

"Say that the Zebesians, under Ridley's influence, became super-aggressive... Would that really lead to the resurrection of the Space Pirates? Without a malicious force to lead them down that path,"

Again, she is referring to the Space Pirates being a galaxy dominating terror, which Ridley was not responsible for when he alone led them. They've only been at that level of a threat when led/controlled by Mother Brain, the Ing, or Dark Samus.

And remember, she's referring to the man-made Cyborg Zebesians.

In the past both Mother Brain and Ridley were referred to as the leader of the Space Pirates, though in Metroid and Super Metroid it was Mother Brain who was the final boss.

Metroid Fusion manual page 5.

Super Metroid opening.

Super Metroid manual page 5.

The Super Metroid comic would show Ridley and the Zebesians as subservient to Mother Brain, where she would order them around. Ridley would also have to propose ideas to Mother Brain instead of simply acting on his own.

Super Metroid comic chapter 4, page 5. Via MetroidDatabase.

The Manga clarifies that Ridley originally led the Pirates, but when Mother Brain came into the picture she was the overall leader while he was delegated the role of "leader in battle" or battlefield commander:

Metroid manga vol. 2, chapter 9, page 17. Translation via Metroid Database.

When Ridley leads the Pirates they are mostly just that, a gang of pirate ruffians that cause terror in the galaxy, but when Mother Brain leads them they are a well coordinated militia capable of truly dominating the galaxy. 

This difference is what Samus was referring to when she suggested Ridley couldn't lead the (Cyborg) Zebesians down a path to revive the Space Pirates.

CLAIM 4:

"Other M changes how Samus felt about the infant Metroid/hatchling (called "Baby" now for some reason). Previously she didn't really care for it, only seeing it as a potential energy source to help humanity, which she gave to scientists for study, but she didn't really care for it. Now she's depicted as caring a whole lot for it"

Samus's relationship with the Baby was not just from the ending of Metroid II where she found and took it with her to the beginning of Super where she gave it to Ceres Station for study, but largely shaped by the events in Tourian at the end of Super.

Their history started when Samus was ordered to exterminate the Metroid race. She went through SR388 killing every Metroid, including the Queen Metroid at the end. She then finds one more Metroid egg, it hatches and the Baby comes out. It doesn't attack her like the rest, instead it clings to her like a child would to a mother.

Believing its study could benefit humanity, she gives it to Ceres, where Ridley later steals it (worth noting "Ceres" is from the Roman goddess of fertility and motherhood)

After making it her mission to recover the Baby, Samus eventually encounters it again in Tourian where it's significantly larger. It attacks her and nearly kills her, but then seems to recognize her and let's her live.

Samus makes her way to Mother Brain and fights until she is forced to her knees. Samus is about to die when the Baby comes to attack Mother Brain. The Baby drains energy from Mother Brain and uses it to restore Samus. Mother Brain attacks the Baby, and then it makes a final charge when it is killed. Its remains fall on Samus, who now has the Hyper Beam given to her by the Baby. She uses this new power to destroy Mother Brain and escape before Zebes explodes.

The species Samus was meant to exterminate was now the only reason she could save the universe. This last, galaxy saving, Metroid is now destroyed.

This is the context for why she has a deep connection to the Baby in Others M.

Even before these events it's not as if she didn't care for it, as she was unable to bring herself to kill it even though she is a hardened bounty hunter:

Super Metroid manual page 4.

Both the Japanese & English guidebooks/comic depict Samus caring greatly about the baby Metroid:

Samus is depicted as crying at the Baby's death and furious at Mother Brain for killing it. Super Metroid comic chapter 5, page 5 (as listed on Metroid Database).

Via the Second Office of Trentesse section of Super Metroid's JP guidebook. Translation via Metroid Fandom wiki.

Other M is merely following up on the existing narrative between Samus and the Baby started in Super (& its guidebooks).

The Baby having an emotional effect on Samus in Other M was not some arbitrarily forced thing, but a continuation of a plot thread started years ago.

Samus's hesitation to kill another baby Metroid in Other M is because of the effect the Baby had on her. This species she spent years killing, now revealed the potential to care for and protect her? And give her powers needed to save the galaxy? Should this species really be exterminated?

Fusion would show Samus had sentimental feelings for the Baby when she learned its DNA is what saved her from the X-Parasite:

Via Metroid Fusion opening cutscenes.

Also, Other M didn't change the name of the Baby Metroid from "infant"/"hatchling" to "baby" as it was always called "baby" in the Japanese versions of Super and Fusion:

Examples of "baby" used throughout Super and Fusion.

Katakana chart with "ベ (Be)" and "ビ (Bi)" circled (used for "Baby").

"Baby" was also used in some English Metroid media as far back as 2003 such as the Metroid Prime section of Nintendo GameCube Preview Disc, the timeline section of Prime's Bonus Disc, the Fusion art gallery unlocked in Zero Mission, and Super Smash Bros Brawl:

Top left via Nintendo GameCube Preview Disc, top right/middle via Metroid Prime Bonus Disc, bottom left via Metroid Fusion gallery, bottom right via Super Smash Bros. Brawl's Ridley trophy.

CLAIM 5: 

"If Samus learned the Federation were illegally cloning Metroids in Other M, then she shouldn't have trusted them again in Fusion"

Firstly, Prime 3 showed Samus had already read about spies within the Federation, so she would've known of some corruption already, before even the events of Metroid II/Samus Returns:

Left via the Bryyo Falls logbook entry , right via the Taking Valhalla logbook entry

Secondly, just because some members or sects of a massive organization like the Galactic Federation are corrupt does not mean the whole of that organization is. In Other M Samus learns that the programs on the Bottle Ship were illegally conducted, which means it wasn't officially approved by the whole Federation.

Thirdly, Fusion already set up that Samus must've been suspicious of the operations on the B.S.L. Station, specifically of the possibility of a Metroid breeding program.

Via the cutscene near the end of Fusion.

CLAIM 6:

"Other M's Queen Metroid shouldn't exist, as a Queen could only evolve on SR388 or a replica of its environment as seen in Fusion"

Nothing in the series actually states Metroids are incapable of evolving outside of SR388 or a replica of its environment. What's said is SR388's ecosystem is "ideal for raising" Metroids, not that it's the sole ecosystem capable of producing evolved Metroids.

Via the cutscene near the end of Fusion.

On the B.S.L. Station in Fusion, it was only Sector 1 (SRX) that was stated to be a replica of SR388's ecosystem, no other part of the ship is stated to replicate SR388.

Metroid Fusion manual page 18.

At the end of Fusion we see the Omega Metroid evolved on the Docking Bays, which isn't a replica of SR388's ecosystem, which means Metroid evolution can indeed occur outside SR388's (replicated) environment.

3 Metroid molts are seen in SRX, while the last is seen on the Docking Bays.

The Prime series shows that, at least when exposed to Phazon, Metroids can evolve on other planets (albeit different evolution forms), e.g. the Phazon Metroids' various lifeforms seen in Prime 3:

From top to bottom: Phazon Metroid, Hopper Metroid, Hatcher Metroid.

Even IF SR388's ecosystem was needed to evolve Metroids, the Queen could still exist in Other M. It can be deduced the sect of the Federation in charge of these illegal programs are one in the same in Other M and Fusion, and if they could replicate SR388's ecosystem for the Metroids in Fusion, then what would stop them from doing so in Other M?

The Bottle Ship, where Other M takes place, was constructed to sustain life from various planets, further showing the Federation's capacity to build a SR388-like environment if it were needed to evolve Metroids.

"The ship was made able to sustain three distinct closed habitats, each designed to preserve various specimens collected from different planets for research and development in military-technology applications". Via the computer Maurice and Adam look at in Other M.

Via the cutscene in the Exam Center.

Again, this answer isn't needed as Fusion already showed the Omega evolved outside SR388's ecosystem.

CLAIM 7:

"Other M isn't consistent with how Samus's suit works. Not only does it show she needs to concentrate to summon the suit, but it also shows when she's unconscious the suit disappears, where as Fusion showed her suit stayed on when unconscious"

Since Metroid 1 Samus's suit was shown to be summoned on/off at will.

Via the best ending to Metroid.

Super also shows her suit being summoned on/off at will with Crystal Flash, an ability where Samus manually despawns her suit to concentrate in order to recharge herself.

Example of Crystal Flash used in Super.

The details of her need to concentrate was expanded upon in both the Super comic and the Manga, where it's shown if she is emotionally distracted/disturbed then her suit may not work properly, and can indeed despawn due to her lack of focus/concentration.

Super Metroid comic chapter 4, page 4

Metroid Manga EX (color version) vol. 1, chapter 2, page 9.

In a 2003 Q&A, Sakamoto commented on her suit needing mental fortitude to summon.

Via Zero Mission JP website's FAQ, translated by Metroid Database.

Prime 3 shows her concentrating to summon the suit.

Via the opening cutscene to Prime 3.

Even SSBB showcases this with Zero Suit Samus's Final Smash.

Power Suit Samus trophy from Super Smash Bros. Brawl.

Other M shows Samus use an ability similar to Crystal Flash called Concentration where she can recharge her health and missiles.

Samus concentrating to recharge. Via Metroid Fandom wiki.

The "emotionally distracted/disturbed" context is what Other M shows when her suit despawns.

Samus was emotionally disturbed by several things such as her PTSD being re-triggered by Ridley, fears that her best friends could possibly betray her, seeing another infant Metroid that stirred memories of the Baby Metroid which greatly affected her and now having to steel herself to kill this new baby Metroid, etc. This emotional unbalance is why her suit despawned in Other M and not something like Fusion.

In Fusion she was more so knocked out or forced unconscious by an X Parasite, where she didn't have all these negative emotions swelling up inside her.

Being knocked unconscious and being emotionally unbalanced which causes her suit to uncontrollably despawn are different contexts.

Other M also showed her suit despawning when she was fully awake during the Ridley scene, which further cements it's a matter of emotional balance rather than simply going unconscious.

Battling her PTSD, Samus struggles to maintain her Power Suit.

CLAIM 8:

"Other M acts like the Prime series didn't happen when Samus says she hadn't worked with the Federation since leaving them"

This is a misunderstanding of a quote from Samus in Other M where she says:

"It was the first joint mission I'd been a part of since becoming a freelance bounty hunter. And, of course, it was the first time since my Federation days that I was following the orders of a commanding officer."

She's specifically referring to being in a joint mission with the Federation, as unlike most games Samus isn't hired as a bounty hunter in Other M, but temporarily made part of 07th Platoon under the command of a Federation CO (Adam Malkovich).

This context is what separates it from something like Prime 3, where although she worked side by side with the Federation, she was a hired bounty hunter and not under direct orders from a CO.

This is set up in Fusion when she states:

Via Samus's monologue after obtaining the Fusion Suit.

Other M is the first time while Fusion is the second time.

To further demonstrate how these contexts are different is in the opening of Fusion where Samus was hired to protect researchers on SR388.

Via the opening cutscene to Fusion.

This mission is obviously not the same one Samus later mentions where she was working with her previous CO (Adam) and is under the same context as Prime 3's "hired bounty hunter" while the rest of Fusion is the same context as Other M's "working directly under a CO".

Most Metroid games are under the context of "hired bounty hunter" where as Other M and Fusion (B.S.L. mission) is "directly under a CO".

Other M's own guidebook (JP) has a timeline where the Prime series is included:

Japanese original (top) and Google Translation (bottom).

CLAIM 9:

"Samus being scared of Ridley makes no sense considering she's fought him several times at this point and had no issues. Maybe this could've worked as a prequel, showing her first encounter with Ridley, but not this late in the timeline"

Samus isn't "scared" of Ridley in Other M, she's having a panic attack brought on by PTSD.

Before I go further I want to discuss what PTSD (Post-Traumatic-Stress-Disorder) is. I'm no expert on the subject, but I do understand it's a very serious thing many people have to deal with, and for many it can be difficult to fully overcome. Here's a few descriptions of PTSD and its symptoms:

What is PTSD?:

"PTSD (posttraumatic stress disorder) is a mental health problem that some people develop after experiencing or witnessing a life-threatening event, like combat, a natural disaster, a car accident, or sexual assault.

It's normal to have upsetting memories, feel on edge, or have trouble sleeping after this type of event."

What are some symptoms of PTSD?:

"There are four type of PTSD symptoms: reliving the event (nightmares, flashbacks, or triggers), avoiding situations that remind you of the event, negative changes in beliefs and feelings, and feeling keyed up (hyperarousal). Symptoms may not be exactly the same for everyone. PTSD symptoms usually start soon after the traumatic event, but they may not appear until months or years later. They also may come and go over many years. If the symptoms last longer than four weeks, cause you great distress, or interfere with your work or home life, you might have PTSD."

Who develops PTSD?:

"PTSD can happen to anyone. It is not a sign of weakness."

Here's a video which goes over PTSD and CPTSD.

Of course, this being a real and serious thing many deal with on a regular basis, I'm not attempting to diminish that in favor of the discussion of a video game, obviously the treatment and help those who struggle with trauma can get is more important than a video game. I just wish to set the precedent of this being a real thing that real people, no matter how strong, deal with and how this game interprets/depicts that.

Though response to trauma seems to be personalized and not always consistent, I want to show excerpts of an interview involving a real war vet and psychologist regarding the PTSD scene in Other M:

Koehne: "That is very much so how PTSD works.... you daze out of it for long stretches and your brain seems to freeze and do its own thing or render you basically useless..."

Dr. Grohol: "Mental disorders like PTSD are recognized disorders of brain and behavior that have decades worth of research and are based upon thousands of peer-reviewed studies. It is no different than having a disease like diabetes or Parkinson's.

Interviewer: "This scene has caused a row amongst the gaming community. Some feel she has PTSD, and others say that she should be able to “get over it” as she has fought him before and won. Can one simply “get over” something if it causes PTSD?"

Koehne: "A story answers this for my point of view. I watched a man burn to death and pulled guard on his body so we could retrieve the remains and not let the insurgents disgrace the fallen soldier by dragging his body around the streets. To this day I have a problem with barbecues which used to be one of my favorite things to do.... I still do BBQ every now and then.... but things have changed!!"

Dr. Grohol: "If someone experience a trauma at an early age, such as having someone kill their family, then something like post-traumatic stress disorder (PTSD) is indeed a possible reaction. One does not simply "get over" a mental disorder because these are not choices we make in the first place. Who would consciously choose to be depressed, or to have PTSD? It's an absurd argument"

Interviewer: "How realistic would a situation like the above be, or being a work of fiction, was it handled incorrectly?"

Koehne: "That is a great depiction of PTSD... and just to think soldiers have to deal with that in real life fights..."

Dr. Grohol: "Someone who was in a situation where they had something to trigger a flashback, as what appears to occur in the video, could very possibly react in a similar manner -- frozen in place, being unable to act or react for a time. Flashbacks themselves can be traumatizing, and different people will experience and react to them differently. The reaction of the character in the video was consistent with the way some people might react to meeting -- once again -- a murderer they thought they had previously killed"

It does frustrate me sometimes when people don't seem to understand how PTSD works, and they can't even understand a fictional portrayal of it, that the idea of a strong person could have a "weakness" like being susceptible to trauma is just not possible, that it's "unrealistic" for fiction to portray it this way, as if no real life strong person could ever have this so-called "weakness".

Jessica Martin, who voiced Samus in Other M, stated she related to Samus's trauma as she herself had experienced a trauma before recording for Other M. She saw Samus as being someone who was "so strong" despite being traumatized.

Going back to the game, we can see the in-universe context as to why Samus has PTSD: when she was a child she witnessed Ridley murder her parents and destroy her colony on planet K-2L. Witnessing this traumatized her.

This aspect of Samus's story was first introduced in the Super comic, though Ridley was not cited as directly responsible (it could be implicitly inferred as he is the "leader of the Space Pirates" and it was Space Pirates who were responsible for the raid on K-2L).

Super Metroid comic chapter 4, page 2. Via Metroid Database.

Super Metroid comic chapter 4, page 3. Via Metroid Database.

The comic would also depict Samus as waking up with nightmare induced sweats (which can sometimes be linked to PTSD), as she had dreamt about being killed on a mission.

Super Metroid comic chapter 1, page 1. Via Metroid Database.

Super Metroid comic chapter 1, page 2. Via Metroid Database.

Later Super Smash Bros. Melee would describe the events of her past on Samus's Classic and Nintendo Event exclusive Trophies.

Via Metroid Fandom wiki.

The first Metroid game this story appeared in was Metroid Prime in both its manual and the original NTSC version's logbook entry "Hatchling's Shell", and though Ridley is yet again not explicitly said to be responsible for the K-2L raid, the same inference I mentioned before could apply here.

Prime manual page 8.

Via the Hatchlings's Shell logbook entry from Prime 1.

On top of this is further suggestion Ridley was responsible. Upon first seeing Ridley, Samus is seen visibly angry (and perhaps anxious) where she's shown to be rapidly clenching her fist and then shaking her arm violently, we then see a furious look in her eyes.

Via the cutscene when confronting Ridley on the Frigate.

Zoomed and slowed to focus on her rapid hand clenching.

This is not a reaction Samus gives to just any enemy, but only to Ridley.

The Metroid Manga would explicitly show Ridley being responsible for the raid on K-2L and the deaths of Samus's parents.

Manga EX vol. 1, chapter 1, pages 25, 30-31, and chapter 2, page 2. Via Metroid Database.

This left Samus with trauma, which developed into PTSD.

We're then shown Samus's first reaction to seeing Ridley again after her childhood, where she would meet him in her teen years and become mentally unstable at the mere sight of him as her PTSD is triggered.

Manga vol. 2, chapters 8-10 (abridged to focus on Samus's trauma). Via Metroid Database.

Manga vol 2, chapter 10, pages 10-12. After a lengthy traumatic episode, Samus would eventually compose herself with the support of others. Via Metroid Database.

Years later at the end of the manga, Samus would encounter him again (same encounter seen in Zero Mission). She is depicted as having resolved herself enough to not break down at the sight of Ridley.

Manga vol. 2, chapter 16, page 20. Via Metroid Database.

(Some have said this scene in particular shows why she wouldn't be "scared" of him anymore in Other M, but I'll get to that later.)

The Japanese release of Fusion would have new ending images which shows the backstory of her parents being killed by Ridley and her upbringing by the Chozo. These images would later be unlockable in the English release of Zero Mission.

Via the JP ending images to Fusion (unlockable in Zero Mission outside Japan).

Zero Mission would add new scenes not seen in the original Metroid, one scene is Samus's reaction to Ridley where we see a sort of anxious look on her face as she prepares to combat him.

Via the scene before fighting Ridley in Zero Mission.

This look she gives is only in the Ridley cutscene, which further shows her unique connection to him, and not to other monsters she faces.

Prime Trilogy's art booklet contained a story recap of the series up to Prime 3. This goes over the raid on K-2L, the death of Samus's parents, her upbringing by the Chozo, and her personal vengeance against Ridley.

Via Prime Trilogy booklet page 1.

As already shown, even Super Smash Bros. Brawl touches on this, where Ridley's Trophy states "As the culprit behind the murder of Samus's parents, the connections with Samus run deep".

So with all that in mind, the context for Other M is after Samus defeated Ridley in Super the whole planet of Zebes blew up on his remains, as Samus recounted in the opening of Other M:

"And the explosion that followed destroyed planet Zebes, along with the remains of Mother Brain, the Space Pirates, and my long-standing nemesis, Ridley. And the baby..."

Because of this Samus believes him to be truly dead and gone (which is true as the "Ridley" seen in Other M is a clone, unbeknownst to Samus at the time of their meeting).

Before encountering Ridley Samus was tracking the Mystery Creature, so when Ridley appeared before her she was caught off guard as the "impossible" happened; Ridley back from the dead. This was the being that murdered her parents she had spent years trying to kill, and finally succeeded when Zebes blew up. She had finally put that part of her life behind her.

Now he's here, alive, which is why she says "Ridley?! No! It can't be!", even Adam utters "Huh? What the-?" when seeing Ridley.

(Samus's "No! It can't be!" is unsubtitled, but heard at 0:30)

Some fans have suggested this scene contextually only works as a prequel, showcasing Samus's first encounter with Ridley after the K-2L raid, and that "it doesn't make sense why she wouldn't have an issue before fighting him several times in the series already" but the context of Other M doesn't work as a prequel, it's specifically designed as: "Ridley has died, now he's back (via cloning)"

To this, some may say "Well he's died before and came back, Super is no different".

What makes Super different from his other defeats is his body literally explodes into multiple pieces, and then Planet Zebes explodes on those remains.

Ridley's body explodes into several pieces upon his death in Super.

On top of his defeat by Samus, Ridley's remains are then destroyed by the planet Zebes exploding.

Whilst Ridley is very tough to permanently put down, he's not some literally immortal being incapable of death. If that were the case then the Pirates wouldn't need resuscitate him in Prime, which shows he didn't actually die in Zero Mission.

"resuscitating Mother Brain, Ridley, and Kraid". Via Prime manual page 9.

"After his defeat on Zebes". Via the Meta Ridley Pirate Data logbook entry in Prime 1.

Ridley surviving can be deduced for all his defeats, where he was badly defeated but never truly killed, until Super.

At this point many question his defeat in Prime 3 where he appears to explode into a puff of Phazon dust (though it's not entirely clear what happens).

Via the cutscene after defeating Omega Ridley in Prime 3.

I would first like to say that this is the Prime series, a sub series to the main Metroid games, as such it's up to Prime to explain how Prime fits with the Metroid series. Any possible issue caused in Prime is a fault of Prime, not the main series. That being said I don't believe this is an issue. If Ridley is alive by Super then that means he didn't die in Prime 3.

Though there isn't an explicit statement that says exactly how Ridley survived his defeat in Prime 3, the biggest clue is Phazon. Phazon is not only capable of healing injuries when used in the right context, but it can quite literally regenerate someone who has been blown to Phazon particles (like Ridley appeared to have).

Dark Samus disperses into Phazon particles similar to Omega Ridley.

Dark Samus later reforms herself with Phazon.

Though some people believe this ability is only used by beings of pure Phazon, Dark Samus was capable of regenerating short of complete atomic destruction before becoming pure Phazon. This means Ridley could potentially use Phazon to regenerate himself from being blown to Phazon particles in a similar way.

By the second battle with Dark Samus, and before she became pure Phazon, she was already capable of reforming her body with Phazon. Via the second logbook entry for Dark Samus in Prime 2.

It wasn't until the final battle did Dark Samus become pure Phazon, reaffirming one doesn't need to be pure Phazon to regenerate from near atomic destruction. Via the fourth logbook entry for Dark Samus in Prime 2.

The Space Pirates, Ridley, and Samus herself all made use of Phazon to heal and regenerate.

Via the Omega Pirate logbook entry in Prime 1.

Via the logbook entry for Omega Ridley in Prime 3.

Via the Phazon pool scan in Prime 3.

Via the Ultra Phazon Unit scan in Prime 3.

The reason why Samus could still believe Ridley to be alive after Prime 3 is that she knows of the regenerative powers of Phazon after witnessing and using it first hand, as such she could deduce Ridley could have regenerated after their battle and before she destroyed Phaaze.

From what we see in the series, as an adult Samus had been able to resolve herself against Ridley during the end of the Manga/Zero Mission battle and we can assume she used this resolve in the other battles against him (though Prime shows she still isn't perfectly calm when facing him). It's not until Other M that Samus is explicitly stated to believe Ridley to be truly dead and gone. With Ridley not alive anymore, it can be assumed she wouldn't need that resolve she used against him anymore (as he's gone now).

The belief he's gone and she wouldn't have to face him anymore, coupled with him appearing out of the blue, is what re-triggered her PTSD. She not "scared" at having to fight an enemy again, but is having a reaction to deeply rooted trauma. There's a big difference.

END:

I hope I've been able to clear up some of the misconceptions around Metroid Other M, and that maybe you now have a better understanding of the game (and perhaps the series as a whole!).

Throughout the post I used links to videos and websites as a way of crediting those whose videos/images I used for some of the content in this post. The images/gifs/videos without links were from my own copies of the games/booklets.

Thank you for reading! See you next mission 👍