An ion drive was a type of engine. They characteristically pulsed, allowing K9 to detect one when it was nearby. (TV: Underworld)
The spaceship Shadow had an ion drive system, including an "ion chamber". (TV: Enlightenment)
The exodus ships that left Red Rocket Rising and were subsquently destroyed by the Daleks ran on ion drive engines. When these ships were blown up, "what you [got]" was ionotronic dust. (AUDIO: Blood of the Daleks)