- Grey and Gray Morality: Particularly the end, where you have to choose between Central undergoing Grand Theft Me and going underground to help her sister fight against Nina or Central assisting her erstwhile foe in a Mind Probe of Central's own sister. Your mileage may vary in determining which is the "good" ending.
- Nightmare Fuel: Regis and Lao's meeting with Giel. They arrive to find his partner shot dead in an indoor jacuzzi and Giel himself torn to pieces and splattered all over the bedroom. Eventually they find out what happened: Giel drank wine spiked with powerful hallucinogens and shot his partner thinking he was some kind of monster, then screamed at his robot maid that something's inside him and she needs to get it out. With the maid's safeties disabled, she complied. Graphically.
- The "human resources" trojan that can hijack your brain, force you to fly to China and turn you into an obedient sweatshop worker. Though the scene with a victim being only partially hijacked by one, with the trojan posing as an obviously fake version of him in Trance while trying to browbeat the real victim into submission with propagandist slogans, is played for comedy, the implications for a total hijacking are pretty horrific.
- Spiritual Successor: Arguably one to Beneath A Steel Sky, especially considering how the network interface sequences are set up.
- The Woobie: The suicide bomber. Aside from just being a teenager, and all the brainwashing and mental conditioning that would make him willing to blow himself up, he also has to walk around on crutches because the biological engineering to make his bones grow explosives instead of calcium comes with a myriad of health problems, which he's had to deal with his entire life. He also screws up his mission and ends up trapped in an empty monorail car, lamenting that he's failed in his purpose and will now have to blow himself up while accomplishing nothing. Fortunately, Regis can talk him down and get him to surrender to the police to get his life back on track and hopefully gets the explosives removed. Unfortunately, Central has him euthanized instead.