- How did Adam get uploaded to the computer after he sacrificed himself in Sector 0?
- The way it was phrased, it sounds like important personnel in the GF have their minds uploaded on a regular basis (like backing up your hard drive every week). The AI 'did' ask how Adam died.
- Why on earth (wakka wakka) does a space station need a boiler room? The problem should be getting rid of excess heat, not making more of it.
- Justified by Sector PYR as a whole, specially because there are creatures that requires excessive heat (Norfair-tier) to live!
- How is Samus able to swing from monkey bars when one of her hands is covered by the arm cannon?
- Either a magnetic grip or the arm cannon morphs into a hand and back instantaneously.
- Okay, so the X realize Samus is a major threat to them because she has Metroid DNA now, allowing her to absorb them like a Metroid would. In order to combat this, the develop the ability to lower their 'bodies' to extremely low temperatures which seriously harms Samus should she try to absorb them. An interesting way to show the X aren't just mindless killing machines but it begs the question of why they didn't do this with the Metroids way back when the Chozo designed them to be their natural predators.
- Aside from needing extremely cold environments in order to change them, what makes you think that they didn't? The later metroid instars aren't particularly vulnerable to being frozen.
- The X didn't just arbitrarily lower their temperature, they used Sector 5 to do so. SR 388 has never been stated to have regions with low temperatures, and even if it did it would only significantly affect larval Metroids.
- Why is the Omega Metroid actively trying to kill you in the finale? With Metroid DNA, it should view you as a curious sibling, if nothing else.
- Larval Metroids might not have the intelligence or sensory organs to tell that Samus isn't a real Metroid, but Omegas are fully grown.
- It's also possible that the Omega Metroid had killed a few of the SA-X copies previously and saw Samus as just another one of them.
- Another possibility is that it was a fight for dominance. The Metroid DNA they used to start the breeding program and to create the Metroid Vaccine were taken from the Baby Metroid, and Other M confirms that the Baby Metroid had the genetics necessary to become a Queen Metroid.
- Why is the Arm Cannon on the Fusion Suit rifled (check some of the promotional art)? It's primarily a directed energy weapon and its missiles are fin-stablized. The former is unlikely to gain a spin, much less benefit from it, and the latter would if anything be better off without a spin.
- Why doesn't Samus mutate? The environment of SR-388 is what causes the Metroids to mutate and transform into Alpha, Gamma, Zeta, and Omega forms, so why didn't the now part-Metroid Samus undergo any sort of similar mutation?
- Likely due to the amount of time spent there being fairly mininal, the remnants of her suit separating her body from the external environment, or just that she is not metroid enough to metamorphose.
- At the end, when Samus absorbs the SA-X, does that mean that going forward she can no longer absorb X-Parasites or worse, can be infected by them again?
- That's unlikely, considering that none of the other X Parasites that Samus absorbs up to that point have any effect on her ability to absorb X.
Headscratchers / Metroid Fusion