An Arm and a Leg: He lost his legs and an arm due to severe injuries from a tragic accident.
Badass Bookworm: Alistair may be a man of science first, but he's got one hell of a (metal) left hook, and when he's at full mental capacity he can hold his own in a fight.
Gadgeteer Genius: Alistair built all the robots in Shark Reef Isle himself.
Mad Scientist: He doesn't consider himself this at first, but when Julia name-drops the archetype, he does accept the label as reasonably accurate.
Nice Guy: Alistair's clumsy attempts to woo Julia and his Character Development over the course of the novel reveal that he is actually this at heart, and was probably even more so in his previous life.
No Social Skills: Ten years of virtual solitude will do that to a guy.
Julia Parker
Broken Bird: She suffers from PTSD due to a traumatic event from six months before the novel opens.
Good Angel, Bad Angel: A variation. Julia hears the voices of "the sensible one", who gives her professional advice on her situation, and "the rat one", who rudely berates her behavior and choices.
Psycho Ex Boyfriend: What he becomes after he is turned into a cyborg. There were shades of this pre-cyborging, too, especially since he set Julia up to be attacked because he thought she was going to break up with him.
Yandere: When he was sure Julia is forming a relationship with Alistair, he goes on a psychotic rampage, preferring to kill them both than lose Julia to another man.
Arthur
Robot Buddy: When he communicates through a drone.