it pretty much goes without saying that Shepard isn't allowed to go off into danger without Kaidan.

i don't have much input otherwise since you did a super job laying everything out, but as far as the inciting incident, iiiiiiiif nothing less horrifying comes along, I could potentially arrange for Kaidan to poke his nose somewhere he shouldn't hacking-wise and get him in trouble with Hypatia, or have him... uncover something he could bring to Shepard?