Dr. Watson in the Institute would like you to obtain blueprints from the Brotherhood of Steel. The randomly designated location of this quest will be shown after you accept the assignment.
Regardless of your allegiances, there are no repercussions for killing members of the Brotherhood of Steel in this quest. However, it's also easy to spare them and focus on your objective, given that the blueprint is marked on your waypoint indicator.
No one has to die in this mission since the blueprints are in a crate, not someone's possession. Return to Dr. Watson with the the blueprints to complete the mission.