Agree that the ending isn't gelling with the rest.
To me it feels like a non-ending of the weak sort; you build it up with the interesting logs and hints of more going on… and then it kills two agents and is never seen again. That sort of "so we still have no clue what's going on here" ending can work, but it's very hard to pull off. Kudos if you can make it happen, but sometimes a little bit of explanation can go a long way. Right now you're ending on a weak answer: "it doesn't like the Foundation", when you could be ending on a strong question ("what does this thing really want, and why?") or even following it down the rabbit hole into higher planes of weirdness.
One of the Foundation's specialties is applying scientific curiosity to the anomalous, trying to figure it out:
Can they attach a tracking beacon to it to figure out where it goes when it isn't active?
Maybe weld it in place, so it's considered part of the vehicle and won't get left behind?
If they figure out where it goes, what do they find there? Further weirdness? An anomalous warehouse? A normal parking lot?
Can they put a tire boot on it, or remove its tires so it cannot drive off, or tow it away?
Can they get a better look at the driver by flying a drone-mounted camera directly up to the window?