Unmarked spoilers below!
- The backgrounds are much more detailed this time around, including the presence of large living creatures or robots that sometimes move around. However, there is a huge, red-eyed... something
◊... inhabiting the background of Area 4. And it looks ready to attack Samus at any second. Given the nature of the planets Samus explores, you'd think this would happen, but it luckily doesn't. - In Area 3, you come across a grapple point that must be ripped away in a quiet room. Doing so ends up reactivating a giant Chozo mining robot called the Diggernaut. It looks at you with its single, glowing red eye ominously before going on its way. You meet it again not much later in Area 4... and now it's trying to kill you from the background when every other background character has been seemingly docile. Getting grazed by its mining drills during the Advancing Wall of Doom sequence is a One-Hit Kill, and you only get the machine off your back by hiding in a Morph Ball-sized notch in the wall and letting the Diggernaut think it killed you. You don't get to fight it directly until the end of Area 6, and even then and after receiving more defensive upgrades, this robot, not specifically designed to be a death machine, is still a force to be reckoned with.
- The music for the segment of Area 6 past the triple crumble block climb is just...weird. It almost sounds like there are deep male voices saying things with the fluctuating background sound, and it just overall sounds very ominous. Quite unsettling.
- The Zeta Metroids were redesigned from being Ugly Cute chubby dinosaur things to essentially Xenomorphs now.
- The Omega Metroids got a similar redesign treatment in that they went from a moderately-intimidating dinosaur-like creature◊ with a Lamprey Mouth to a humanoid lamprey with some dinosaur traits◊. They are now as big as the one in Fusion, can move surprisingly fast, and are strong enough to cause the ceiling to crumble just by slamming their tails on the ground. The first Omega's introduction cutscene? It marches on into a room that was once seemingly Metroid-free when you were hunting the other Metroids in Area 6 with no warning, trampling a shed skin in the process, and we don't know what Metroid that skin belonged to. Their "Psycho" Strings-filled boss theme lets you know that other than the Queen, they are the apex predator of SR388.
- You know how the Chozo used to be Proud Warrior Race Guys but gave it up and became pacifists? The secret 11th Chozo memory reveals that there is a warlike rogue faction of Chozo who didn't hesitate to kill fellow Chozo. The Red Filter of Doom really gives the idea of how bad the situation is.
- And then there's the transition to this secret memory when it's first unlocked. The theme music in the background becomes garbled and peters out as the tenth picture morphs into the eleventh. Some viewers might have thought a horror Jump Scare was about to happen the first time they saw it, and scrambled to adjust their audio in time.
- The mere fact the game shows there is a 10-limit memory, until after a few seconds of unlocking the last one, the transition just happens out of nowhere and adds the 11th memory.
- This 11th memory isn't just a look into the dark side of the Chozo race, it's the first glimpse of the Big Bad of Metroid Dread, Raven Beak. For Samus Returns players transitioning to Dread, it gives them a pretty good idea of what to expect from this new villain.
- You know how in AM2R, there is an utterly inhumane scream by the Queen Metroid when you kill your first Omega Metroid? Here, if you kill all the larvae Metroids in the final area, the Queen will roar when you near her location. Again, she is not very happy about you killing her children.
- The Queen Metroid's new boss music. Gone is the catchier tune from the original game and AM2R—replaced with remixed bits of it, Mother Brain's theme from Super Metroid, and a menacing orchestra all mixed into a terrifying cacophony of a song only befitting such a monstrous creature.
- Proteus Ridley. While his sudden appearance is more awesome than frightening, his appearance is somewhat unnerving when you look at the implications. In Metroid Prime 3: Corruption, (Omega Ridley) was last seen retreating, as an exploding mass of Phazon - and considering that the Prime games take place all before this one, Ridley not only survived the extreme Phazon withdrawal from his body, but has continued to regenerate his body as normal even afterwards! Once he is defeated, his cybernetics short out - which initially would have one believe that he would slowly die out without them. But as the ending goes to show, that isn't the case: he just shed them all anyway. They don't call him "The Cunning God of Death" for nothing!
- The Stinger after the Final Boss. We see a green Hornoad hopping around, minding its own business, and then we see a familiar-looking, floating yellow blob begin getting near it. The Hornoad hops away from it and eventually leaps behind a pillar. The blob follows and ambushes it. We don't see what happens, but we do hear the poor creature's pained shrieks. The next time we see the Hornoad, it's turned red, has grown several spikes, and it lets out a vicious roar. It's a disturbing scene, and you know what's worse? YOU allowed it to happen!
