An advanced AI named "The Three Magi" (which are 3-programs which vote for strategic effects) exists in the show. Without going too much into details, a problem occurs in the AI, so the lead scientist Ritsuko steps into the machine to check things out.
She comes with a circular saw. She cuts open one computer (the one named "Caspar") ... revealing to the audience that inside is a living brain, hooked up to a bunch of wires: https://imgur.com/MTZ7pzU
This is the first point where the audience probably starts to wonder about the ethics of the main characters. The later reveals of their bio-engineering / morals are more horrifying. But this is perhaps the audience's first look into the inner-workings of the NERV organization / science that they do.