كُتِبَ الدَّرْسُ بِالْقَلَمِ — The lesson was written with a pen.
كُتِبَ: past passive.
الدَّرْسُ: nominative passive subject.
بِالْقَلَمِ: bāʾ of instrument plus genitive noun «الْقَلَمِ».
The prepositional phrase is not automatically the passive subject; it expresses an instrument.