Brain is a bunch of connected neurons with inputs-outputs.
Let's simplify it to ONE neuron only to illustrate how the desicion is made. Neuron has many (sometimes many hundreed) inputs and one output. If total signal on all inputs exceed certain threshhold value, neuron switches to excited state and generates output signal.
Now, let's say that one input comes from eye, another one from ear, another one from memory, etc... If total strength of all signals is below threshold, the output signal is zero (pilot flies directly from A to B without changing course). But if there is strong signal from memory (honorable discharge is around the corner) or from ear (intelligence guy reported that guerillas were seen in that forest half way from A to B just two days ago) or from eye (bunch of ducks is suddenly right in front) - the neuron switches to excited state and joystick gets a command to change course.
Or if there are weak signals from ear, eye and memory (weak enough to not switch neuron separately - pilot may even not recognise any single suspicious factor - what we call below "conscious" level), but their sum is more than the threshold value, neuron is switched "on" and the pilot's hand is turning joystick away from straight flight "just in case". You may call it "subconscious" decision, but there is no physical/mathematical difference between the two situations.
Pilot may have too little information about his dangerous mission, and far from discharge, and thus total signal from all incoming nerves can be below threshold and as the result the neuron will not be excited. Then helicopter flies directly from A to B. But what a misfortune - it is right over guerilla's site and it is missiled down. And now barely survived prisoner of war (pilot) memorises that he did not read carefully intelligence report which warned about possible movement of guerilla to this place - thus the tiny missing bit of voltage on one of the many inputs made the fatal difference of not exciting the neuron and of making wrong decision (to fly straight).