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- The Shimmer itself. A strange, complex alien entity that does not one bit adhere to the law of physics as we know it, emanating a ever-growing dome of radiation that horrifically mutates every lifeform it comes into contact with and creates vicious, disgusting monsters that live in unbearable pain. Even though certain aspects of it are serene or even beautiful, namely the deer with cherry blossom branches for antlers and the crystallized trees on the beach, it's clear that the Shimmer's presence on Earth was horrific and very much destructive. Had Lena not destroyed it, it would have eventually enveloped the entire world, bringing annihilation by endlessly mutating everything to death and essentially giving the Earth cancer.
- What's even worse, if its core being comes into contact with a human being for long enough to fully absorb their DNA, it assumes a human shape that mimics the movements of the person it imprinted on, and further contact results in it becoming a full on clone of that person, including some of their memories. It's left entirely vague whether the Shimmer is a malevolent entity seeking to destroy everything out of irrational hatred, or if it's so utterly alien to the point that it doesn't comprehend its own existence in the way an oversized cancer cell would. By the end, our two main characters are either clones created by it, meaning the Shimmer lives on in them, or they have been so fundamentally and genetically transformed by exposure to it that they are now a new species.
- The bear monster pictured above, which has a Skull for a Head and whose roars are mixed with Shepherd's dying screams.
- The Facial Horror of this monster doesn't stop there. If you look closely on the left side of its skull, you can see a human skull growing out of it. Even worse when you consider that the creature already absorbed Shepherd's DNA, it's very likely that the skull is from Shepherd herself.
- And just when you thought it couldn't get worse, one of the eye sockets of that human skull? It has an eye in it. Which is mobile. And has the same eye color as Shepherd.
- The way it dies is not any pretty either, getting an assault rifle emptied into it at borderline point-blank range, creating a gigantic hole on one side of its head. Pretty Little Headshots averted like hell.
- The worst thing about it is that, despite being mixed with Shepherd's DNA and mind, this is not a case of It Can Think. The way it mimics Shepherd's voice doesn't seem to be a conscious predatory act to lure in its prey, as all of its vocalizations sound like that even after it's snuck up on the team. So what we're hearing is not a sadistic monster tormenting the humans, but a wounded animal (possibly even one with some fragments of Shepherd's mind still in there) moaning in agony.
- When the bear attacks Anya, it kills her by graphically ripping her lower jaw out. The suddenness of the act makes it all the more jarring.
- The Facial Horror of this monster doesn't stop there. If you look closely on the left side of its skull, you can see a human skull growing out of it. Even worse when you consider that the creature already absorbed Shepherd's DNA, it's very likely that the skull is from Shepherd herself.
- As the team enters the military compound there can be seen large, colorful lichen/moss-like growth on the concrete walls. The camera almost gently narrows in on one for audience to see it moves. And then it turns out that one of the previous team's soldiers was partially assimilated by it, leaving behind only a skeleton.
- Mutated human remains, such as a person who was seemingly turned into a human-shaped tree with flowers growing on it, or another one merged into alien fungus growing on a wall with his missing skull nearby.
- The trailer's unsettling, alien-sounding leitmotif. Which not only appears in the film but completely takes over the score during Lena's climactic encounter with the Humanoid. That blaring, distorted trumpet sound is so inexplicably creepy.
- The deaths of Cass and Ana are relatively straightforward but horribly gruesome (compared to the other more mind-screw style horror of some other scenes). Being torn to pieces by a bear does that.
- The last time we see Josie, her arms are sprouting leaves and red rosebuds at a slowly-yet-steadily increasing pace, implying that she may have turned into one of the human-shaped flower bushes, like the ones the group encountered earlier, shortly after Lena loses sight of her.
- The two Apocalyptic Log videos left by Kane's earlier expedition. It's ambiguous even to Lena's team if they indicate that the earlier team went insane, or if the events actually happening to them inside the Shimmer truly were that surreal.
- In the first, Kane vivisects another soldier to reveal the changes his body is undergoing. The soldier is apparently willing and perhaps Kane is trying to help him (gently holding his head with one hand as if to reassure him, then cutting a square out of his belly with a knife). Kane then peels open his belly to reveal what look like live, eel-sized worms writhing around in there - possibly attached to his body, mutated out of his intestines - or something (it might have been his mutating body restructuring itself really, really fast). One of the worst parts is that there's no screaming at all, and the soldier might not be able to feel pain anymore. From start to finish, it's unclear if Kane himself is insane or not.
- The second and final log crosses into Mind Screw territory, with Kane inside the lighthouse, struggling to describe the changes coming over him. And the person filming the scene is Another Kane, apparently the one who returned to Lena in the beginning.
- That scene with the doppelgänger. That weird tone on the teaser trailer? It's the sound the thing makes as it's manhandling Lena to presumably absorb whatever it needs to copy her.
- More probably, it didn't even realize it was hurting her. The shot plays out almost like a sexual assault, but as Lena notes when questioned, it simply mirrored her own movements. Lena pressed herself against the door and the creature did the same, likely unaware that she was trapped by it - which is no less frightening.
- While the ending of the movie crosses can be seen as both Bittersweet Ending mixed with Ambiguous Ending, the original ending was a straight up Downer Ending. Because even though Lena managed to destroy the Shimmer, thus seemingly saving the world, after it's revealed that her and Kane are either clones or simply new beings mutated, it pans out to a space view of Earth, and we see several more meteors falling to Earth, which ultimately meant Lena's efforts and the deaths of everyone else were All for Nothing, therefore Earth's annihilation really is guaranteed.
