BTW, its the manual for Fusion that states that that all enemies encountered including the pirates on board the BLS were 'test subjects'. Even the 'research zombies' (were either test subject slime creatures or x mimicking the research team) .
I barely remember other details in the game... All I can remember was it implying that the Federation were working on metroids (from DNA taken from the Child Metroid from Samus Suit IIRC) as a potential bioweapon use. I don't remember anything about pirates in cahoots directly... By the time you encounter pirates in the game, they are all infested or x-mimic creatures.
As mentioned the manual only mentions the two 'native SRR-388' creatures encountered in the game. Hornoads and Arachnus.
There is at least a suggestion elsewhere that Biologic was an "organization which studies dangerous creatures from distant planets." Which suggests that they were collecting creatures from more than SRR388. It just happens to be that 90% of the creatures in the game are those that appear on Zebes. Several more that also appear in the various 'Prime' series planets as well
Its interesting that the "Zebesian pirates" that appear in Fusion are also rather 'bird-like' similar to the Chozo. But appear to be wearing bug-like armor..
Yes, and it is explained in the lore that such bioweapon research was illegal according to Federation law, which is why areas in Fusion like the Metroid breeding project were heavily restricted areas you can't get to until later. The whole point of Metroid II is these things aren't supposed to be researched and need to be wholly exterminated. Samus's altruistic thought to hand off the Metroid baby in Super comes back to bite her in the ass right after she departs Ceres, and her home from ages 3-16 gets blown up. Lesson learned. Not to mention Adam gives her shit for it.
Fusion also states that the Federation didn't ask for or expect her help on the BSL station, which is why they stopped sending her data once she started snooping around in the wrong places and saw they were up to no good, and A.D.A.M. tried to lock her in a room under orders from up on high. It's also confirmed by the shadowy figure - implied to also be the Colonel from Other M - who appears twice in attempts to cover up the Metroid breeding program.
Remember also that BSL contains all of the Metroid variants except for the Queen, so it's not just those few enemies from SR388.
So it was the first game to imply that the Federation types were doing things they shouldn't be and were trying to keep it quiet.
The Chozo/"Zebesian" pirate thing I've explained elsewhere, and why I hate the use of the term "Zebesian" because it's inaccurate and grossly misleading. Think of them like "processed" Chozo, not unlike how the Collectors in Mass Effect are genetically modified Protheans who serve the Reapers. Same idea. They are not native to planet Zebes and they're only called that because Sakamoto doesn't double-check the lore before he writes whatever he wants.
Didn't one of the games suggest that there are quite a few 'brain computers' like Mother Brain?
Aurora Units in Metroid Prime 3: Corruption.
There really aren't that many Metroid II enemies in Fusion (2-3 tops? Hornoad, and the Arachnus). Most of the enemeis in the game are ripped out of Super Metroid. Then again get reused in Zero Mission.
Interesting information about Urtraghus but apparently it was a scrapped idea created for Prime 3: Corruption, and never used. What material even discusses the planet visited in Prime 3 just calls it 'one of the pirate's homeworlds'.
So that many fans just consider the details as 'non-canon' since it hasn't been used officially yet.
Sort of hard to 'retcon' anything if the material was never officially released in the first place.http://metroid.wikia.com/wiki/Pirate_Ho ... ite_note-1
And considering the number of convoluted internal lore edits that prime trilogy underwent over the course of the series... during its various localizations... It hasn't been internally consistent. Requiring its own retconning, and retconning lore surrounding information it has in relation to old trilogy material, that has created some of its own plot holes. Like the existence of Metroid inside of the Phazon asteroid. It was originally a Metroid that the pirates brought to the planet, that escaped entered the asteroid and somehow helped spread the phazon that it started to produce in its body. To later localizations changing it to a Metroid that travelled to Tallon IV on board the asteroid from Phaaze. Metroid Prime being from Phaaze, yet metroids were created by Chozo, but never discovered Phaaze.
There are a number of chicken or the egg paradoxes created as the series went forward.
This lead to the need to predesignate the metroids in Metroid Prime series as Tallon metroids, since they are weaker and different than classic series metroids.
But that's not saying the original non-prime series is necessarily 'consistent'. Other M introduces a few plot holes and its own inconsistencies IIRC as well.
The Metroid wiki - as I have said before - is a poorly-maintained, fan-made project which asserts many things that are either fan-canon or even fan-art as official. A lot of information there is wholly incorrect. Don't treat anything it says as gospel. It's one of the leading reasons most fans aren't really up to snuff on basic canon and where Sakamoto twisted things. IIRC Urtraghus was used in the Japanese localization but not the English Language one, in which it is just referred to as the "Pirate Homeworld".
Regarding the use of the term "official," Nintendo does such a poor job with this IP they slap things around willy-nilly, including all the different versions of Samus's origin which they interchangeably decide are official when they're in a certain mood and someone shows up at the office in a green tie. That doesn't change the fact that among all the different stories, there are some events which make more sense linearly than others, and from that we can piece together a more "proper" timeline so long as we treat the Yokoi/Kano stuff as foundational canon and rewrite Sakamoto's toilet-paper writing to properly fit that world-building.
Aurora Units do appear in Fusion as well, if I recall correctly. If I'm not mistaken they can be seen in the background tiling of one of the levels. The BOX bosses in Fusion also have AU-like brain components.
This was always meant to support the notion that corrupt portions of the Federation were working in service to the Pirates, and recloning their forces after their losses, explaining how Mother Brain could reappear in Super Metroid after just two games before she was, well... pretty dead. And yes, Mother Brain is some form of primitive Aurora Unit (at least, that's the implication). IIRC A.D.A.M.'s module inside of Samus's ship is also a cloned brain in a jar inserted into the ship's hardware, but don't quote me on that one, I may be confusing that with official concept art I saw for something else (I work in this industry so I see a lot of stuff).
We know the Pirate hierarchy communicates telepathically so it's somewhat implied that the Mother Brains Samus has fought are not the real deal, but "proxy bodies" telepathically controlled remotely, explaining why the two subsequent resurrections of the character still had the same MO instead of being born a blank slate.
As for plot holes and inconsistencies or chicken-and-egg paradoxes, not so much, unless you regard Zero Mission as canon, which you shouldn't. It was a novelty made as a cash grab, but is anachronistic in the time line, and the instruction manual description of the story spits on Kano's lore so hard it's not even funny. The only real problem with Prime is it doesn't fit neatly between the first 2 games and was crowbarred in, whereas it would work better as a sequel series.