I've played both games pretty recently, so no, I think I'm fairly up to speed.

Let me put it this way. Let's take a couple examples from Prime 3, for instance, what she does while she's on Bryyo. She arrives with orders to destroy the seed and be on the lookout for Rundas. Those are her two main orders, and that's all she's required to do. The Federation contacts her from time to time with "you'll probably need to do X in order to accomplish that order we gave you earlier," such as telling her she'll need to disable the anti air cannons to take down the second seed shield generator, but it's not a direct order.

In fact, most of what she receives "DURING THE WHOLE GAME" is advice from the Federation. "You can get the hazard suit to protect yourself here," or "here's how to assemble a bomb that would make the process of getting to the seed easier." There's a big difference between "you must do something" and "here's some stuff that will make your job easier."

Allow me to illustrate with some direct quotes from the game. Here's a sample of what the Aurora Unit says to Samus about certain things.

"There are two anti air craft turrets protecting the generator. Your ship will not be able to get a clear shot while those guns are active."

"Samus, we have discovered a Federation landing site on Bryyo. You may be able to use this facility to upgrade your ship."

"Samus, Gandrayda's communication capsule has revealed intel concerning the Pirate facility. We believe there is a cargo supply route that connects directly to the seed. The gate in the command courtyard appears to be its main entrance. It will be impossible to go through that area unless you can find protection from the acid rain."

"Samus, Unit 217 has discovered evidence of hidden Chozo artifats on Skytown. Perhaps these could assist you in accessing the rest of the Pirate base."

The similarity between all of these is they are advice or suggestions. "Samus, it looks like there's something obscuring your path" or "here's something that might help." She isn't told "go upgrade your ship here" or "go look for those artifacts." It's passed on to her as a bit of information, and she can do with it as she wishes. Obviously, the game forces you to do all of this to complete it, but that's besides the point; from a story standpoint, Samus could technically find another way around it and the Federation wouldn't care.

In Other M, meanwhile, Samus is given very direct orders from Adam all the time. These aren't suggestions. "Samus, activate your Varia Suit." "Samus, investigate the Bioweapons Research Facility." "Samus, look for survivors in Sector 2." "Samus, use your Plasma Beam." These are all commands. Every single one is something Samus must follow through. In Prime 3, the Federation couldn't care less if Samus has an upgraded ship or the Hazard Suit or whatever, so long as the Leviathan gets destroyed. In Other M, Adam would (presumably) be upset if Samus just shrugged off one of his orders. Everything Samus is given in Other M is a command. The vast majority of what she's given in Prime 3 are suggestions.

HOWEVER

Even if everything she had been given in Prime 3 was a direct order, it still wouldn't matter. Here's why. How many of the objectives in Prime 3 involve cooperating with the Federation army? In fact, how much of anything she does involves direct contact and cooperation with Federation Troopers?

Nearly nothing at all. That's the point here. Samus consistently interacts with the Federation troopers aboard the Bottle Ship; she's told to investigate that one facility in Sector 1 with the troopers, she takes down a boss monster with the troopers, she meets up with Anthony on a number of occasions; she's consistently operating with the Federation. She hardly ever does that over the course of the Prime series; the one segment with protecting the troopers is all that comes to mind, and that, as I mentioned before, probably wouldn't stick in her mind as a full mission.

Even if Samus was being given direct orders and being forced to to fill them out to the letter, it wouldn't make a bit of difference because she's hardly ever directly cooperating with other Federation troopers. Simply filling out orders from someone else isn't a joint mission, it's a contractual relationship. She has to actually be interacting with Federation troopers/personnel on the ground doing the same task that she is in order for it to qualify as a joint mission.

HOWEVER

Even IF Samus had been doing all of that, if she had been receiving direct orders from the Federation all the time and had been consistently interacting with Federation personnel on the ground, it STILL wouldn't make the Prime games non-canon. Why? Because the one line we're all so worried about here is from Samus' perspective. She could easily simply not view her time in Corruption as a joint mission, or have simply misused the word in her head, or only qualify something as a mission if she believes she'll be consistently interacting with other Federation troopers, or any other number of possible explanations. How Samus refers to something when she's thinking isn't a definitive be all end all description of how something actually is. If Sakamoto, for instance, had said that Other M was Samus' first joint mission, defined joint mission in the terms you're thinking of, and all of the previously mentioned requirements were met, then yeah, maybe that would mean something. But what Samus is thinking in the heat of the moment, and not knowing what she considers to be a joint mission, that's an entirely different story. It's an incredible leap in logic to take that one sentence and say "Clearly Other M intended to make the Prime games non canon."

Again you fail to understand how Adam and Dane orders affect the way Samus carries herself in the mission, of course Dane could easily say "There are two anti air craft turrets protecting the generator. Take them down now." just like Adam does, and the other way around, Adam could make suggestions and say "Samus, Ridley is to strong for your current arsenal, maybe you should try a different weapon" but he doesn't because he doesn't respects Samus as Dane does and He should. The notion is the same, a joint mission but with two completely different characters at the lead of the mission, one that respects Samus and one that doesn't. Another point, what's the main fail in other m? Samus character desing, no way in hell should Samus take the orders and commands Adam tells her. In prime 3 Dane knows Samus won't obey every single order but in Other M her character was so changed that she suddenly takes every single order and she acts how Adam wants her to act, unlike prime 3 were she is told what to do but she can do it anyway she wants, again, because Dane respects Samus and Adam doesn't, and in Other M she suddenly obeys orders and acts how she is told to act, not how she wants.

And please, are you actually telling me Samus interacts more with the galactic federation in other m than in prime 3? Without counting Adam and Anthony you only see the other dumb troops once or twice and then they become COMPLETELY IRRELEVANT. If we are talking about interaction with irrelevant troops, then she has way more interaction in prime 3 as I can just visit random troops and talk to them at any point of the game. And the troops in prime 3 helped WAY MORE than Adam, Anthony and the other idiots. Remember the WHOLE FEDERATION, NOT JUST THE TROOPS SAMUS HAS TO PROTEC, INVADED the space pirates homeworld and they did A LOT MORE than Adam, Anthony and the others COMBINED because they actually HELPED SAMUS IN AN IMPORTANT MISSION, unlike the useless characters in other m. My point is in prime 3 not only does Samus interacts way more often with the galactic federation, THEY ARE TREMENDOUS SUPPORT TO SAMUS DURING THE WHOLE GAME TO THE POINT THAT THEY HELPED HER TAKE DOWN THE SPACE PIRATES. In othe m not only are ALL THE CHARACTERS IRRELEVANT, THEY NEVER HELP SAMUS AT ALL, AND IF NINTENDO RESPECTED SAMUS A LITTLE BIT MORE SHE WOULDN'T NEED ADAM AND COMPANY AT ALL AS SHE ALONE COULD COMPLETELY DESTROY THE BOTTLE. 

And last, Nintendo made the prime series non-canon (intentionally or not) the moment they decided to support this game full of horrible plot holes, a terrible story and BY FAR the worst portray of Samus character ever.

The operative word is he "could" say that, but he doesn't. Until he does give a direct command to do so, it doesn't qualify.

And no, I'm not telling you that Samus interacts with the GF more in Other M. What I'm telling you is that Samus cooperates and acts towards the same goal with Federation troopers (i.e. the very definition of a joint mission) far more in Other M than in Corruption. Even without direct cooperation, Samus' objectives in Other M are basically the exact same as the soldiers; search the ship for suvivors. In Corruption, the only time they are the same are the "protect the troopers" mission. She destroys the seeds without any cooperation from soldiers, she boards the Valhalla and takes control of the Leviathan without any cooperation from soldiers, and she invades Phaaze and destroys Dark Samus without any direct cooperation from Federation soldiers. The objectives she's trying to accomplish are always different than the ones the Federation soldiers are pursuing; i.e. not a joint mission.

The last point about making the Prime series non canon would make the entire series non-canon as well. I agree Other M's portrayal of Samus is terrible, but as far as canoncity is concerned, it's just horrible writing and nothing more.

Last reply because you clearly don't get my point on Dane and Adam. Both Samus and the federation cooperate together to Invade and take down the pirates homeworld (joint mission by your definition) that alone is MORE cooperation on a BIGGER scale and FAR MORE IMPORTANT that the cooperation Samus had with Adam and crew (which was none because as I said Adam and company are COMPLETELY IRRELEVANT). So even if you don't want to recognize the whole prime 3 game as a joint mission, you can't deny that the invasion to the pirate homeworld (not just samus protecting the troops) is a joint mission, as both the federation and samus fight together to take them down, and that mission alone is more important than whatever interaction you think Samus had with Adam and the others because they don't help her at all. Take Adam and the others and you know what happens? Samus finishes the mission faster. Take Dane and the federation and you know what happens? Samus has a harder time taking down the space pirates (not saying is impossible because is Samus and she can do anything).

And that girl is? 

I get your point on Dane and Adam, the problem is that, for some reason or another, the definition of a joint mission simply isn't connecting with you on some level.

Let me put it as clearly as I can. For something to be a joint mission, the two sides have to be doing essentially the same thing. The assault on the Pirate Homeworld does not count because Samus isn't ever shooting Space Pirates with any Marines (with the exception of when she's babysitting the bomb troopers). After the babysitting stuff is done, Samus (once again) goes off on her own to do something entirely seperate (in this case, blow up the Leviathan) while the Federation handles the actual fighting the Space Pirates.

To put it simply; the Federation is fighting the Pirates on the ground, Samus is fighting Ridley and blowing up the Leviathan. Two entirely seperate tasks. If Samus had, for instane, joined up with some Federation platoon and the entire team had taken on Ridley, then that would be an entirely different story. But Samus goes off on her own to do something else entirely different while the actual main battle takes place elsewhere.

And, yes, take away Dane and Samus would have a harder time, sure. One side making things easier for the other doesn't equate to a joint mission, however. I'd have a really hard time getting to school were it not for people paving roads, but that doesn't mean I'm in a joint mission with the Department of Infrastructure.

Perhaps the biggest point in all of this, though, even IF that qualifies as a joint mission, I still see no reason to suddenly dismiss the whole Prime series as non-canon when there are far simpler explanations for a single line of dialogue. Samus may not have considered such a small portion of her task to be a joint mission. Or she may simply have not been thinking. Or she may have been thinking of a joint mission in the context of following a more rigid structure like she had back in the Federation. There are far more simpler and much easier explanations than jumping to the conclusion that that one line of dialogue was intended to undermine the entire Prime series.

I'd argue that your definition of a joint mission is fairly incorrect in many real-world contexts. Many would call the Korean War a NATO joint mission but it was mostly American troops. In Iraq US and British troops weren't necessarily doing the same thing, which does not mean it's not a joint mission. Just two examples for the sake of discussion. Not saying anything about that canon-breaking line in Other M, mind you, I'm just making a point where I see an issue.

Personally I'm of the "Samus forgot" explanation, since she sort of seems to forget a couple things about being Samus. (Zing!) Seriously, though, I do lean towards the "Sakamoto screwed up/didnt care" explanation and I pay one sentence no mind. Although now that I think about it, is the translation exactly taken from Japanese, or were there changes in that monologue? Because that could possibly explain the issue.

I'll certainly grant that, my definition is more of one coming from how Samus seems to be coining the phrase. By the loosest term of the phrase "joint mission," one could call Samus being sent to eradicate the Metroids on SR388 a joint mission, since it was funded by the Federation, and, going by the NATO example, funding from another group can be enough to consider something joint. Obviously the game seeks to keep Metroid 2 canon, so there's some deeper level of connectivity/cooperation that Samus has in mind when terming things as a joint mission.

This whole debate has certainly dragged on long enough, though, so I suppose I'll hold my peace and end by saying that one line, especially one as vague as that, shouldn't and almost certainly wasn't meant to undermine the Prime series as canon. The dialogue, I believe, was originally written in Japanese and translated to English, so I don't know what the original phrasing as Sakamoto wrote it was or meant. Simply going off the English version, though, there just isn't enough there to undermine the Prime games as canon. Even if you accept that the Prime games contain "joint missions," so to speak, Samus as a character views things differently, and I find it much more likely that she either forgot, views the term differently, or thinks of a joint mission as something far more formal than her previous ventures than assuming that Sakamoto was plotting to take down the entire Prime series through one sneakily placed line.

Nice thread, as a Metroid fan, count me in!!!

The best Metroid game this generation will be Super Mario-troid Maker.