better late then never:
it's been a while since i last used hammer so i might get a couple of bits wrong, but i used a func_tracktrain entity (not to be confused with func_tanktrain). i created a series of nodes for it to visit in it's route, and then checked the option to have it teleport back to the first node.
at different nodes i set up logic for it to do things like, stop at station and open doors. It kills any aliens in it's way by using a trigger_hurt that's parented to the front of the train (gets turned off when the train is stationary) set to do 10000 damage. make sure you make the trigger big enough so that the aliens die before the train actually touches them, or the train will get stopped until they are dead.

depending on what you want your train to do, you might be able to use a func_movelinear, or even a door entity (i.e. if you want it to move in a straight line only)