At Spin Two Swords
A ship moving through space is generally a glaring emission of radio waves and heat. It is spotted almost all of the time by these two signatures. Visual confirmation is possible at long ranges but is fairly difficult. The sky is big and ships are small.
As the name implies, a ship running silent is operating with relative stealth. It is not transmitting radio signals, either outwardly towards space or internally amongst its crew. Having aimed at its destination, it cuts maneuver jets and simply stays at its current velocity. A ship may take this a step further and actually turn off all electronics if it is desperate to avoid being discovered. This extreme is known by spacers as running at full silent.
While running silently, characters cannot use active sensors like radar. Moreover, they cannot generally use active communications. Trying to get a signal out, generally involves a difficult Comms roll (between -1 and -6, but generally -2). Often, this roll requires that the other side “listen” in a certain way. It doesn’t matter if you modulate frequencies if no one else knows the frequency of your modulation. A thorough listener may discover that there is something wrong with the message they’re receiving and look into it more, but this is unlikely, takes time, and really only matters with repeated messages (like SOS beacons).
Running Silently also means that the ship will take a lot longer to get wherever it is going (the effect is more pronounced for longer journeys, and is between 150-300%). Remember: a ship uses its maneuver jets up until the point when it needs to decelerate. Running silently means not running the jets and continuing at the current velocity. Plotting a course while running silently generally involves an unmodified Navigation + Education roll.
The effect of running silently is pronounced. Basically, the ship can still be seen by all sensors, but at increased difficulty. A ship running silently is at -4 to be seen by Thermal sensors (-6 if full silence), -4 for EM (-6 if full silence), -2 for Active Radar (-4 at full silence), and impossible to detect with passive radar. Visual, NAS, and Densitometers detect at normal.