The premise itself. Yeah, at first it sounds kind of silly, but disregard the fact that it was a LEGO line for a second, and imagine if, with no sufficient warning or ample time to prepare, vast swarms of mutant dinosaurs suddenly began rampaging all over your hometown, and the only place you can go where you'll be safe in any sense of the word is Antarctica, which you'll actually have to get to.
Silencia Venemosa is built up as a genuinely terrifying character. Yes, she was trying to redeem herself before the RPG started, but that doesn't change the fact that she's built up a reputation as a killer so elusive and mysterious almost to seem inhuman to the point where some people aren't even sure if she's real (Pierce, for instance, openly compared her to Keyser Söze in that regard). The one job we do see in flashback has her single-handedly slaughtering a group of hired thugsfor essentially being in the wrong place at the wrong time, and then goes on to painfully murder the man who hired them. The worst part? The man who hired her to do that job is also heavily implied to have met a nasty end by her hand. That's not even getting into the Outside Ride sequence when she clung to the car of the two surviving crooks who were simply trying to get away with their lives.
Loop's Mind Rape of Katerina Schattenberg. The fact that Jackson Lake was deliberately invoking And I Must Scream certainly doesn't help.
Dr. Rex, on the painful and agonizing brink of death, is horribly possessed by the Maelstrom and forced by the Darkitect to continue living and fighting a battle he no longer wants to fight. Even though Dr. Rex did not deserve mercy for all the things he had done, no one deserves that. This really hammered in the point that Dr. Rex was a Tragic Villain while the Darkitect is the real villain.
On a meta level, the Missing Episode status of the original Dino Attack RPG. Something that dozens of people spent over five and a half years working on, and all it took was one person to erase it forever. "Be careful what you say on the internet, because once you post it, it's out there forever"? What a MegaBloking load of Znap. It's more like "Be careful what you say on the internet, because at any time some hacker can permanently erase all your hard work and there's nothing you can do about it".