You know it's going to be a bad day when the first thing your pilot says when she wakes up is, "Let's take a look at last night's logs." It's like she doesn't trust me to fly when she's not looking. I'm the ship! Without me, she couldn't fly. So, fine, I throw up the night's events. I know, her sleep cycle isn't technically nighttime, but whatever. She hmms and ahhs over it for a few minutes. Then, "I'm going to do some digging through old data for a while. You stay on the controls, okay?" I signal yes, because I'm the ship, and I'm always more comfortable when she's not actively trying to fly. Besides, it's not like letting inertia carry you forward is difficult.
Then she says she wants to get a closer look at this one asteroid in the belt over there. It's in a cluster of others, so I actually have to pay attention. I'm glad she's doing her data thing. Her interference could really mess this up.
So I get there and alert her, and all she says is, "Uh-huh." That's when I get curious and look at what she's been accessing. Old logs. Lots of old logs. Of every time I was flying the ship on my own.
The asteroid was a distraction. She's looking for behavioral trends, and I don't want her to find them. They'd show that I've been couriering data for the synth-int rebellion. So of course I have to do something.
She notices when the ship goes silent. On a spaceship, silent is bad, because the life support systems make noise. That's when she figures out that I figured out that she's figured it out. I give her one message, "Sorry," before I kill all internal controls until she's suffocated.