Commonly used when discussing illnesses or conditions that must resolve without medical treatment. The doctor said the virus wasn't serious and to let it run its course.
Pro Tip 2/3
No Control
Used to express situations where one has little or no control over the outcome. They were trapped in the elevator and had to let the rescue process run its course.
Pro Tip 3/3
Patience Required
Implies that patience is necessary while waiting for the natural progression of events. The cake needs more time in the oven; just let it take its course.