- The destruction of the Earth by an unstoppable asteroid, a creepy eyeless baby, homicidal alien Riders and Blue Meanies, and Kubrick, a character with transparent, plasticlike skin. His original skin was stripped off of him piece by piece by the insane ship AI, Mother. In front of his screaming father. Applegate is either a genius of children's literature or some sort of alien monster that feeds on the fears of tweens who also happens to be a great writer.
- The main characters getting stuck in a painting of hell. And a character accidentally decapitating himself and getting saved by scary worms... And later uses those worms in an act of unintentional cannibalism.
- The woman who is pregnant when she enters the cryogenic tubes and emerges a mindslave with a freakishly-large baby still attached by the umbilical cord who tries to make deals to save the crew in exchange for eating survivors.
- The longest recurring set of antagonists are horrible creatures that nobody sees the face of until book seven or so, the paintings that made up the environment were brought to "life" in a fairly horrific way (the "actors" were automatons who were missing details and didn't bleed). The Bosch paintings were about what you might expect if a mad computer brought them to life as the security system from hell (and Violet stopping to explain everything about the art didn't help). The Triad were really messed up (mentally and physically) and just wanted to kill everyone weaker, prettier, or uglier than themselves. Tamara's Baby was awful on it's own, but when it started communicating outside its host... And wormfood is no longer a synonym for dead. Heck, dead doesn't even mean "lying in place and not moving" any more. And all of it is inside a giant ship that's gone mad with loneliness and only even likes one being anywhere, who's also mad from loneliness. Then they get back to Earth. Things don't get better, just less weird.
- The sapient ship's AI, Mother, is eventually reprogammed by Duncan (?) into a dumb, mindless, enslaved automaton with a hot actress' voice named Daughter. Tate's body is interfacing with Mother at the time and Mother makes damn sure Tate feels all of her pain and rage at having her mind stripped away.
- Tate's mutation, The Mouth. When Tate is cornered or scared, she puffs up into a monstrous version of herself with a gigantic Mouth. A gigantic Mouth that attempts to eat whoever is threatening her. If Tate successfully ingests someone, that person simply does not die. They remain fully conscious but they live inside Tate's body with her, and communicate telepathically with her. Unless Tate is overpowered by their will, and they take over her body instead. At one point, Tate, Yago, Charlie, and Amelia are all fighting over who gets control of Tate's body. Charlie is eliminated (read: driven insane by loneliness and his consciousness ceases to exist) by Tate, Yago, and Amelia teaming up and refusing to speak to him, convincing him that he is the one that's insane.
Nightmare Fuel / Remnants