A stapling instrument system is disclosed that comprises an instrument comprising a handle and an output and, in addition, an interchangeable tool assembly attachable to the instrument. The interchangeable tool assembly comprises a housing, a drive input operably engageable with the output, and an end effector comprising a first rotatable output shaft, a second rotatable output shaft, and a transmission configurable in three operating states which selectively couple the first and second rotatable output shafts with the drive input.