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If you'll notice, at the part where Samus finds the lab with all the metroids, they do not attack her. They instead go after the SA-X. It is often theorized that the reason they don't go after fusion-Samus is because of her part-metroid physiology due to vaccine, and they perhaps think she is one of them.

Taken from the metroid wikia, it says as one of the trivia notes toward the bottom: "Certain aspects of this game are similar to to the movie Alien Resurrection. The main character has DNA of the antagonist alien species (Ripley has Alien DNA and Samus has Metroid DNA), members of the normally hostile alien species don't attack the main character due to their possibly thinking that the main character is one of them, and in the beginning Samus says that she was "reborn". "

What boggles me is if the metroids think she's one of them, then why did the Omega Metroid attack her (since it is a metroid)? I mean we all know that Metroids are the only species that cannot possibly be infected by the X parasite, so it's not possible that an X infection would cause it to attack.
Thread title: 
the sa-x was the bigger threat.
^Answers the first paragraph, what about the Omega Metroid one?
One shall stand, one shall ball.
It answers both pretty well, SA-X was the bigger threat so the Metroids went after it. The Omega didn't really have to choose between two targets, it took out Samus and then the SA-X that showed up. Also, the SA-X is a product of X parasites, Metroids were designed to hunt X. Do the math.
What I mean is why did Omega Metroid take out Samus if she had metroic vaccine in her and Metroids were supposed to think her as one of them without attacking her?
Super Secret Area - Dead Ahead!
Perhaps it was simply more intelligent than the average metroids, and could sense what she was, despite her possibly containing DNA.
Hmm, now you mention it, when she says she was 'reborn', it implies that she was cloned form the original (dead?) Samus, with metroid DNA added, like Alien Ressurection. This might be realted to the apparent clone Samuses in the Other M trailer.
Quote from Tonski:
What I mean is why did Omega Metroid take out Samus if she had metroic vaccine in her and Metroids were supposed to think her as one of them without attacking her?

they aren't supposed to think of her as one of their own. all the dna really does is destroy the x parasites in her and allow her to absorb them.
One shall stand, one shall ball.
Honestly, do omega metroids even need a reason to try to kill things? They're kinda the top dog in the Metroid universe.

Quote from Tonski:
Metroids were supposed to think her as one of them without attacking her?


Says who? Ignoring the fact that vaccines do not work at all like this game suggests, the only metroid-like quality she gained was the ability to absorb X.
That, and her vulnerability to ice.
One shall stand, one shall ball.
Right, and that. You get the Varia Suit so soon after that's brought up I tend to forget about it.
Who knows, maybe she ends up sucking energy out of people and animals. (I think there was a fanfic about that)
As I suddenly get images of a vampiric Samus running aroung the Federation... Not exactly the same thing, but close enough.
Mysteries are slowly becoming extinct.
In the beginning, the Omega decided to attack Samus to get her out of the way, so it could focus on the REAL threat: Ice.
Having destroyed the Ice, The Omega had no reason to attack, but then Samus obtained the enemy.  The Omega fought for its life (and lost [unless you suck]).

This might be easier: Omega Metroid's Point of View. Lets call it Steve.

Steve:What's this thing doing here? *Swats at annoying gun-holding being*
Steve:Good now that's out of the way. OMG! That other being-thing is going to kill me!*Swats again*
Steve:What the hell is that blue thing floating there?(Heard as cannabalistic cries to the human ear)
Steve:Didn't I just kill that thing? (Gets hit) WTF! Another one?
Steve:(Swearing uncontrollably. Presumed to have Tourettes) Dies. Boo hoo!

That's about how it went. I think.
LOL DUDE LOL

A metroid named steve? lol
OMG ANOTHER ONE?
Quote from TheGreenManalishi:
Hmm, now you mention it, when she says she was 'reborn', it implies that she was cloned form the original (dead?) Samus, with metroid DNA added, like Alien Ressurection. This might be realted to the apparent clone Samuses in the Other M trailer.



lol, there are no clones of samus in other m. Metroid: Other M (M:OM) Hmmm, it could possibly be her... MOM


...
Shifty Leader
That M2k2 guy
First of all it's been stated that that girl is not Samus. Just because it's a girl doesn't mean it's Samus or her mother or anyone directly related (else Samus doesn't need to identify herself). I'm surpised nobody's exclaimed so certainly that Remember Me? is her husband.

Secondly, take it to the Other M board, geez.
I think it's more like this.
I'm going to call my Omega Metroid: Bob.

First

Bob:"Man, i'm hungry all that's left that's not an X or another Metroid is....OOOH DACHORA'S AND ETECOONS ON THAT SHIP."

Bob: "YUM."

So Bob, runs to the docking bay and the ship leaves, suddenly Samus show's up, now, if my food left and another Metroid showed up that may have gotten there before me and ate the food, or wants the food in case it comes back, i'd pretty pissed as that's my prey. so bob's like

Bob:"HEY THAT'S MY FOOD I'MA KILL YOU METROID" it can probably sense the other Metroid as Samus.


So it attacks, than the SA-X comes, Bob see's an X that can shoot ice, so Bob gets pretty pissed and goes after the X first, then samus gets ice, and Bob dies.

The end.
once GameFAQs, now Twitch
Quote from interdpth:
Bob:"HEY THAT'S MY FOOD I'MA KILL YOU METROID" it can probably sense the other Metroid as Samus.
Shifty Leader
That M2k2 guy
lulz, too bad Other M takes place before Samus gets the Metroid vaccine.
LOL didn't even notice that
Quote from tomatobob:
It answers both pretty well, SA-X was the bigger threat so the Metroids went after it. The Omega didn't really have to choose between two targets, it took out Samus and then the SA-X that showed up. Also, the SA-X is a product of X parasites, Metroids were designed to hunt X. Do the math.


Only a few larva metroids went after SA-X, the rest were pretty much floating there, ignoring Samus.
Shifty Leader
That M2k2 guy
Perhaps behavior changes depending on evolutionary stage. Perhaps as hatchlings they mainly care about survival, but as Omegas, they're very aggressive, even to other metroids.
Edit history:
MetroidJunkie: 2009-09-07 02:47:35 am
One theory is social class with the evolved stages. Samus would count for larva metroid since she has the DNA of one so the larva metroids would recognize her as one of their own while the Omega Metroid would be furious that an inferior form is invading its territory.
Hm...that's possible, since the Omega Metroid was born a Gamma. It doesn't recognize the larva as one of his friend and attack it to protect his territory.