These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Magnificent Bastard: The NEXUS AI by a long way You stop his nukes firing, he sets them to blow up the area you are in. You go to help your allies, he takes over their base while you're in it, laughing at you all the way. You find a way to stop his program, he takes you over before you can research it. You find your own Nukes, he sends laser satellites to blow you up before you can get the access codes. Lets also not forget his creator disappeared and made the AI in his image, or uploaded himself perhaps and then killed almost everyone and everything. It's not only terrifying, but you have to admire his ability to counter your every move and who feels like a real threat throughout; to the point where one wrong move could fail the mission. Those who played Gamma Mission 8 will understand. And if some of his lines or messages are to be looked at closer, he was alsomanipulating The Project, the New Paradigm and the Collective; evidenced by him ordering the latter to attack you as he fired a Nuke at your base without telling them that and after he captures gamma base he calls the Paradigm and the Collective fools and thanks you for all the technology you recovered.
Actually, when you rescued the straggling Team Alpha survivors, they sort of found out that NEXUS IS Dr Alan Reed. The Synaptic Link technology allows humans to transverse digital worlds while keeping their bodies are kept alive in a life support unit.
Nightmare Fuel: NEXUS, that face, that voice, those eyes, that laughter, the fact he is able to monologue about what he is going to do to destroy you then does it before you have time to react or stop him. The fact he was very happy to kill billions of people. You will be scared of him regardless.