It all depends on the urgency and nature of what DEFCON you achieve.

Normal #1: and the signals are all green and no signs of stopping for a meet or pasenger stop, Just wait, you will get stopped eventually.

Main Resevoir Safety About To Lift #1: get the fireman to run (passenger), or have the conductor (freight) to keep an eye on things while you enter the "yellow zone"

Normal #2: same as normal #1. You will get stopped for something that will allow you to "set out a bad order"

Critical Mass/ Reactor Meltdown/ That Wasn't Chicken Tikka Masala I Ate Late Night #2: If the conductor can't run the train, the fireman's passed out from the gasses you've already let loose, and you feel a crappy situation about to transpire, STOP THE TRAIN and take care of business. Tell the dispatcher you hit got an air hose or got stopped for a red signal, or something...

PS, if you achieve critical mass and stop the train, it's common courtesy to drop back to the 2nd locomotive if you have one. One does not s*** where they live, especially when you have to get the train going again and have to smell that until you hand the train off to someone else (unless of course the next crew to take the train is a bunch of as***les, then of course you leave them a special air freshener).