- Why does the SA-X Freeze you and then shoot you you with missiles? Because you have Metroid DNA and that's the only way to defeat them in every other game.
- Why is Neo Ridley not considered That One Boss in this game when he's been that tough in earlier games? Simple. X-Parasites may have the ability to mimic knowledge, power, and forms perfectly, but, in Samus' words, "They cannot copy the soul." The X mimicking Ridley may have modified his form to be more powerful, but it lacked the pride and sheer hatred the real deal had that made him such a threat in the first place. It was doomed from the start.
- In a brilliant tidbit of Gameplay and Story Integration, this is one of the Metroid games where Samus takes the most damage from enemies, at least initially. It only makes sense that after being partly stripped of her Power Suit and weakened from her X infection, she would not be able to take much abuse.
- This also explains why she's capable of hanging one-handed on ledges without any power-up: since parts of her suit have been removed, she's lighter.
- There is one missile expansion in Sector 3 that is almost impossible to skip without Tool Assistance. However, if you do manage to skip it, the missile expansion will still be gone when you need to go through the room containing it later in the run. Why? The SA-X most likely took it, since it destroys the two doors you would have used to return from the Super Missile data room.
- The second form of the SA-X you fight on the Control deck looks like a cross between Samus and an infected Hornoad. Meaning it is possibly the original SA-X, which infects Samus after the Hornoad it had infected/mimicked is killed.
- The Omega Metroids in Return of Samus were outright immune to the Ice Beam and had to be missiled to death, but the Omega here was the other way around, being immune to missiles (even the Ice Missiles) and needing the Ice Beam to kill. Sounds erratic, but in an earlier conversation, Adam told Samus that the Federation was developing means to accelerate the growth of Metroids; a larval growing into an Omega in days, for instance. Without the years to truly develop the beam-resistant carapace and hide that the naturally-grown Metroids on SR388 possess, the Omega retains the traits its larval form possesses and is thus easily subdued by the Ice Beam. The immunity to Ice Missiles is linked to the larval Metroids' own resistance to missiles, a trait that was lost to the Pirate specimens kept in frigid Phendrana or raised on Phazon.
- The reason Samus looks so different out of her suit compared to pretty much every other out-of-suit appearance is due to the surgery performed on her at the beginning of the game. Since her power suit had already become a part of her, and considering how different the power suit looks afterwards, it would make sense the the surgery would change the appearance of her body underneath the suit as well.
- When Samus is told to beeline from a navigation room to another because there may be over 10 SA-X around the whole station, she is given access to a lot of areas due to her arsenal as long as she avoids going anywhere closer to the Main Sector... However there is no SA-X to be found! Only one, who ambushes Samus at the Bridge. This implies that either Adam was lying or the SA-X eliminated each other to reassure their identity as "Samus"... Until you remember there was an empty Metroid husk in Sector 1. And just what do Metroids eat again?
- The ADAM AI asks Samus the following: "Did this 'Adam' care for you? Would he sit in a safe command room and order you to die?" Criticizing both Adam's negligent treatment of Samus in Other M & Samus idolizing him despite his questionable capability. Even when she backs her statement up by stating how Adam sacrificed himself to save her life, the AI trumps this by berating him for choosing to do so because of the fact that it was ultimately unnecessary, and calls him foolish.AI: When Adam decided who whould live, he chose incorrectly.
- SA-X's ability to be outsmarted and outmaneuvered is a by product of it's life. While it has all Samus' weapons it is without any experience using them in a fight or for exploration. It just blows up whatever is in it's way. The only thing it fights is Samus. It never has to learn to fight in ways other than throwing its power around. And when you get away from it by hiding in a room, you do so in a way that didn't blow stuff up. It can't think of ways to explore that don't involve destroying its environment.
- It never made sense why the Chozo would bother to create a species as dangerous as the Metroids. Sure, theyre powerful weapons, but they devour absolutely anything and rapidly metamorphose into extremely dangerous forms. Why bother with something the headache? This game answers that with the X-Parasites. The enemy that is not only powerful on its own, but capable of becoming absolutely anything. The only possible counter for this species is the ultimate predator: one that can devour anything that lives. The Metroids are a massive threat, but a necessary last resort.
- One of the big plot holes Metroid: Other M featured was the idea that Samus's suit came undone if she fell unconscious. It directly contradicts this game, in which Samus is stated to have lost consciousness and had to have parts of her suit surgically removed. There had to be some sort of middle ground to explain both being true, and this awful realization is one such way: Samus may have been unconscious, but far from unfocused: The infection was causing an intense fever dream, and Samus was fighting for her life in it. In other words, if Samus was not having an X-induce seizure, then she was having a severe nightmare.
- The Etecoons and Dachoras you save at the end of the game are very likely the same ones you could optionally save in Super Metroid. Which means if you didnt save them in Super Metroid...
- After Samus sends the BSL Research Station en route with SR-388 to destroy BOTH, everything is good, the galaxy has been saved once again... Or was it? After preventing the reactor meltdown in Sector 3, Adam mentions the possibility of the X-Parasites trying to destroy the station because Samus is a larger threat to X-Parasites somewhere in the galaxy! This implies there are MORE planets infected by this shape-shifting blob, and SR-388 was only one of them.
- Not likely. Adam says that detonating the station in high orbit may not eradicate the X on SR-388. The Colony Drop was done to ensure the death of every X parasite on the planet and on the BSL station.