The rat sucks. If you're going for Big Boss rank, you're going to have less than 11 alerts after losing the PAL Key, which means it'll be in a rat instead of the drainage ditch.
The first thing to understand is that the rat has one fairly simple circular route that it loops through. This route has the following steps:
This route is laid out through a set of 92 waypoints (about 20 at the ditch, about 30 in the north-west, and about 40 elsewhere), which are the key to the rat's random positioning.
When the area is about to begin, the same random function explained in the ditch article is used to select a random number between 0 and 91. The rat is then placed at the waypoint at that index, and set to move along its route starting from that waypoint. This means that effectively there are 92 variations on rat behaviour, even though they're just different start points on the same single route.
If the rat is alerted by you, it will immediately run to the next vent on its route, and then continue from there. There may be some other unidentified random behaviour that I'm not aware of.