It's mostly a vaccine, but also includes a tracker (I originally had an ending planned where you could escape onto the planet and try to hide, only for her to find you easily and reveal she'd put a tracker in you). And yeah, it's definitely intentional she doesn't tell you - it's an expression of how little she cares about you understanding her motives/actions. I actually based that specific part on vet visits I take my cat to, where I just literally can't explain to her why it's happening - I wanted to capture that feeling but from the opposite end, and also have it be frustrating to the player because...she COULD explain! And you probably WOULD understand! But she just assumes you won't, because she thinks so little of humans.