In Prime 3, Samus and the other Bounty Hunters were hired as a 3rd party to assist the Federation. They weren't under Federation Jurisdiction, but they still had rules to follow, such as when Rundas said "I just received word that the Federation is allowing all Bounty Hunters to use ship-command devices."
(Much like if you invite someone into your home, it isn't illegal for them to sit in your chair, but if you tell them they aren't allowed to and they do it anyway, you might kick them out and not invite them back.)
In Other M (and Fusion), Samus IS under Federation Jurisdiction and was made a temporary member of 07th Platoon. She HAS to follow orders or she could face legal action.
In Prime 3, Samus is given a CHOICE if she wants to do the mission or not (the universe was at stake, so obviously she would try to stop it regardless if the Federation hired her or not).
Aurora Unit 217: "This is a dangerous mission. Will you accept it?"
They gave Samus the option to back out of doing a dangerous mission. Had she been under Federation Jurisdiction and they gave her orders, she would HAVE to follow them or be court-martialed.
It's why at the end of Fusion, after she has disobeyed direct orders, she says "They will hold tribunals and investigations. They will hold us responsible."
Speaking of Fusion, in the opening Samus states:
"My mission on the B.S.L station will be overseen by my new ship's computer. Following the commands of this blunt, computerized CO is something I have to bear, as it was a condition of my taking the ship. For someone who dislikes taking orders, this is the second time I've found myself having to do so. It makes me recall my other CO..."
We find out later that her "other CO" is Adam, meaning the first time she was under the orders of a CO, it was Adam. So Prime 3 wouldn't fit with this because it was Admiral Dane, not Adam in that game.
Samus says "my other CO" meaning her ONLY other CO, prior to the computer, was Adam. Otherwise, she would have said "one of my other COs".
Some people have said that her "first time" under the orders of a CO would be her Federation days. However, this doesn't work because Samus would have gone on numerous missions while under a CO during her Federation days, meaning Fusion can't be her "second time" under orders.
The way she talks about it sounds like it is a rare occasion for her to be under orders, hence why she dislikes it when she is. She's used to being freelance and not having to be under someone.
Other M clarifies this by having her say:
"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."
So, if Prime 3 was her following orders of a CO, then it breaks canon with Fusion, because her first time was under Adam (it's why Samus was HIRED in Prime 3, because this fits with what Fusion established).
We also know that Samus' "second time" under the orders of a CO (Adam) was after she became a bounty hunter, because in Fusion, Samus and the computer talk about the time when Adam sacrificed himself, and in the manga, Adam is still alive AFTER she became a bounty hunter. Meaning Adam died when he was on a mission after Samus became a bounty hunter. (Also, it's stated that Adam sacrificed himself so Samus would live, meaning she was present when he died.)
Plus, Fusion helps explain the difference even further with the opening of the game. Samus says:
"I'd been assigned to watch over Biologic's research team, so I once again found myself on the surface of SR388."
And in the manual she says:
"And because of my experience on SR388, the Federation governor for this sector hired me to provide field assistance on the planet."
Fusion has 2 different kinds of missions. The first being a standard "I was hired" kind of mission (when Samus was hired to go to SR388), and the second was one in which Samus was under the orders of a Federation CO. She wasn't hired. Samus overheard the distress call from the B.S.L. Station and wanted to help, but the condition was that she had to be under a CO (obviously, the Federation didn't want her on the station unsupervised, it's why they only allow Samus to explore the station when they see fit).
In Other M, the Federation had already started an investigation on the Bottle Ship prior to Samus arriving. They didn't hired Samus, but Adam allowed her to stay under the condition that she follow orders.
One final thing to clarify how Other M was a joint mission and how she was added on as a temporary member of 07th Platoon:
Samus says "But having me added on as a member must have disrupted the Galactic Federation's plans."
And at the end of the game, the Colonel says "Unfortunate, what happened to Commander Malkovich. And to think that his entire unit was annihilated..." "Sadly, with them gone, you're just an outsider. And given your unofficial status, I cannot allow you contact with the witness."
Meaning Samus would have official status had Adam and his unit been there, which is why when Anthony comes back, he says "Anthony Higgs, sir. Galactic Federation Platoon Seven. I need to secure the safety of any survivers-- Commander Malkovich's orders, and the purpose of this mission." "Authorized by the chairman of the Galactic Federation, of course."
Anthony has official status as part of the 07th Platoon, Samus only has temporary status given that an official member is still alive. It's why the Colonel was forced to hand over Madeline Bergman to Samus, only after Anthony showed up and made her status on that mission official.
In short, most of Samus' missions are when she is hired by the Federation as a 3rd party, freelance bounty hunter, such as the case with Prime 3. (The guidebook for Prime 3 confirms this where it says she continues her service to the Federation on a freelance basis):
Then there are missions where Samus is under Federation Jurisdiction and must follow the orders of a CO.
Other M is her first time under the orders of a CO (Adam) and she was made a temporary member of 07th Platoon, placing her under Federation Jurisdiction. Fusion was her second time under a CO (outside of her Federation days), and again, she was under Federation Jurisdiction, rather than simply being hired.
I hope this clears up any confusion for those that thought this ignored Prime 3, but in case there are things that need to be cleared up, I will also make a short summary of the timeline of events (from Samus' Federation days to the end of Fusion).
Timeline
After Samus was raised/trained on Zebes by the Chozo, she joined the Federation Police (not the army), and she was under Chief Hardy.
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| Chief Hardy |
Federation Police
Samus went on missions during her time with the Federation Police (along with her teammates, Kreatz and Mauk).
She was known for disobeying orders when lives were at stake (Kreatz says they will have to write an apology).
They even did an escort mission for Adam (who was a General in the Federation Army). Adam wasn't Samus' CO at this time, she was still a Federation Police under Chief Hardy (Kreatz mentions how the Police and Army were mixing jurisdictions).
Zebes is attacked by Space Pirates, and the Federation Army has plans to launch an attack. Samus learns about this and wants to go to Zebes herself (even though that isn't her orders). Adam gives her 48 hours to go to Zebes herself before the Army arrives.
After this mission Samus joins the Federation Army, but the manga skips over this and just says "A few years later" to when she is already a bounty hunter.
Federation Army
Other M however has some flashbacks to when Samus was in the Federation Army (Adam was her CO during this time).
During a rescue mission, Ian (Adam's brother) dies when a drive-unit explodes.
This causes Samus to leave the Federation Army and become a freelance bounty hunter.
Bounty Hunter
Samus went on numerous missions as a bounty hunter, and was considered the greatest bounty hunter.
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| Zero Mission's manual |
Samus was paid for her work.
Prior to Zero Mission, Samus makes mention that she is no longer one of Adam's Federation Officers.
Metroid Zero Mission
The Federation Chairman hired her to go to Zebes and destroy Mother Brain.
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| Zero Mission's manual |
Metroid Prime
The Federation hire Samus to investigate reports of Space Pirate activity.
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| Prime Trilogy booklet |
Metroid Prime Hunters
The Federation hired Samus because of a mysterious message.
It even shows her contract details in the game's opening.
Metroid Prime 2
Samus was hired to find out what happened to the Federation squad on Aether.
Again her contract is shown (proving she was hired).
Metroid Prime 3
Samus and the other bounty hunters were hired to handle the Space Pirate threat.
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| Prime Trilogy's manual |
Samus' work with the Federation has been on a freelance basis.
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| Prime 3's guidebook |
Metroid Prime Federation Force
Samus was hired by the Federation to investigate the Space Pirate's involvement in the Bermuda System.
Samus' "services" implies she is being paid.
Metroid II/Samus Returns
The Federation hired Samus to exterminate all Metroids on SR388.
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| Prime 2's bonus disc |
"Commissions Samus", meaning she was paid.
Super Metroid
Samus actually wasn't hired in this game, she got a distress signal after leaving Ceres Station.
She chased Ridley to Zebes on her own accord.
Metroid Other M
She wasn't hired by the Federation to investigate the BOTTLE SHIP, she received a distress call and decided to investigate on her own.
Adam and his team had already arrived prior to Samus, so if Samus wanted to stay she had to follow Adam's orders (or go rogue).
Metroid Fusion
Samus was hired to provide field assistance on SR388.
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| Fusion's manual |
After Samus was cured of the X Parasite infection, she was sent to the B.S.L Station, but only under the condition that she follow the orders of a computerized CO.
Samus disobeys orders and is now hoping someone will understand what she did.
In summary, Samus has only been under the orders of a CO twice since becoming a freelance bounty hunter, and Other M's "joint mission" doesn't go against what was previously established. In fact, it fits nicely with what Fusion stated.
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