Machine 3.2 Critical Missions

Is anyone else confused by these missions?



First four we are tracking down Veil, and then the fifth we just kill
Exiles in three hideouts, and then it ends without an explanation.



HUH!?

   It seems the Machines see the Cypherites as a system of control.  This is from a document that was found during the Hunt for Morpheus event.

   First Agent: They want to awaken others.
   Second Agent: It is the agreement.
   First Agent: With time, the Matrix will be stressed. It could fail.
   Second Agent: A system of control is needed. One moment... A decision has been made: Do not interfere with the masked humans.
   First Agent: Acknowledged